Dolomitization and Silicification in Syn-Rift Lacustrine Carbonates: Evidence from the Late Oligocene–Early Miocene Duwi Basin, Red Sea, Egypt

Abstract

Studies of early syn-rift successions in the Duwi Basin have revealed repetitive lacustrine carbonate deposits exhibiting regressive sequences and early diagenetic processes. Two main informal stratigraphic units (Units 1 and 2), spanning the Late Oligocene to Early Miocene, have been identified in the area. Unit 1 primarily consists of lacustrine limestone and calcrete deposits that formed in a palustrine environment, whereas Unit 2 is composed of dolomites and cherts, which developed during times of lake evaporation and desiccation under arid climatic conditions. A wide variety of pedogenic features, including brecciation, nodulization, rhizocretions, fissuring, microkarsts, and circumgranular cracks, dominate the carbonate sequence, indicating deposition in a marginal lacustrine setting. Integrated petrographic, mineralogical, geochemical, and isotopic studies of carbonate facies reveal two distinct evolutionary stages in the Duwi Basin, with dolomitization and silicification characterizing the late stage. Their isotopic compositions show a wide range of δ¹³C and δ¹⁸O values, ranging from −9.00‰ to −7.98‰ and from −10.03‰ to −0.68‰, respectively. Dolomite beds exhibit more negative δ¹³C and δ¹⁸O values, whereas palustrine limestones display higher (less negative) values. The upward trend of δ¹⁸O enrichment in carbonates suggests that the lake became hydrologically closed. Trace element concentrations serve as potential markers for distinguishing carbonate facies, aiding with paleoenvironmental and diagenetic interpretations. Our findings indicate that the studied dolomites and cherts formed under both biogenic and abiogenic conditions in an evaporative, alkaline-saline lake system. Biogenic dolomite and silica likely resulted from microbial activity, whereas abiogenic formation was driven by physicochemical conditions, including decreasing pH values and the presence of smectite clays. Tectonics, local climate, and provenance played crucial roles in controlling the overall diagenetic patterns and evolutionary history of the lake basin system during the Late Oligocene to Early Miocene.

1. Introduction

The diagenetic variation of lacustrine carbonates in early syn-rift basins provides important insights into the complex interactions among tectonics, fluid movement, and chemical sedimentation. While dolomitization and silicification processes are well-studied in marine carbonates, their drivers of occurrence in continental rift settings remain poorly understood. The distinct geological setting of rift-associated lacustrine systems introduces multiple potential drivers for dolomitization and silicification that differ fundamentally from those in marine environments. Dolomitization has been recognized in continental, lacustrine sequences in a variety of geological settings [1,2,3,4,5]. This process formed pedogenically in marginal alkaline and Mg-enriched lake environments [6], and it can also be accumulated syndepositionally through microbial activities [7]. Also, silicification is an important diagenetic process of ancient lacustrine carbonate rocks during which the silica minerals largely replace carbonate minerals [2,8]. In addition, silicification may occur as a primary precipitate associated with dolomite in saline, alkaline lakes [9]. Typically, the silica bodies occur as nodules, lenses, beds, or irregular geometries, ranging from a few millimeters to meters long, and they can be found within carbonate beds along their bedding planes [2,10].

The Lacustrine and palustrine carbonate sedimentation was abundant during the Late Oligocene–Early Miocene and accumulated in initiation basins, particularly in the Duwi, Mellaha, and Safaga basins [11,12,13,14]. The lacustrine carbonate sequences outcropped in the Duwi half-graben basin (Figure 1) were deposited on the western edge of a shallow and marginal lake. In general, in low-gradient, low-energy lacustrine settings, minor variations in lake level occurred, and the carbonate facies exhibit strong pedogenic modifications when these regions are exposed to subaerial conditions [15,16,17,18,19]. Consequently, extensive lateral and vertical facies changes complicate facies-sequence analysis [17,18,20]. These outcrops display repetitive sequences, allowing for detailed investigations of local variations in carbonate sedimentation, as well as prominent dolomitization and silicification, which are the subject of this study (Figure 1). Previous studies [11,12,13] demonstrated that these deposits formed within a general shallow lake environment. However, debate persists regarding shifts in lacustrine depositional environments and the rapid facies changes. Additionally, no data exist on dolomitization and silicification in the lacustrine deposits of the western Quseir area along the Red Sea. Therefore, this study aims to accomplish the following: (i) discuss the petrographical and geochemical characteristics of the different carbonate facies, (ii) determine the vertical variations and the factors controlling the transition from limestone to dolomite and chert facies, and (iii) investigate the sources of silica and magnesium, as well as the different formation mechanisms and controls of dolomitization and silicification in lacustrine deposits.

2. Geologic Setting

The northwestern margin of the Red Sea is defined by two major fault systems formed during Late Oligocene extensional tectonics: the Coastal Fault System and the Border Fault System. The Coastal Fault System strikes NW and runs sub-parallel to the Red Sea coastline. In contrast, the Border Fault System, located further inland within the basement of the rift margin, consists of a series of WNW-trending fault segments [13,21]. The hanging-wall structure of the Border Fault System is dominated by a series of half-graben basins. The Duwi Basin, located west of Quseir city (Figure 1), is considered one of the initiation rift basins that developed in the northwestern Red Sea area. It is an elongate NW–SE-oriented basin, extending between the latitudes 26°04″ and 26°22′07.34″ N and the longitudes 33°52′32.08″ and 34°12′11.44″ E. The basin is bordered to the east by the NW-striking Nakheil Fault Zone (NFZ), which reveals the half-graben structural organization [13,21]. The fault is highly segmented with WNW-, NW-, and north–south-striking sectors. The footwall of the Nakheil Fault zone consists dominantly of Precambrian basement except in the southern sections, where it is dominated by Nubia sandstones in the footwall (Figure 1). The hanging wall of the Duwi half-graben basin is marked by several doubly plunging, longitudinal synclines. These synclines vary in width from 4 to 10 km and extend between 10 and over 20 km in length (Figure 1). Their axial traces are either offset or display bends along the strike, closely following the orientation of the Nakheil Fault Zone. The Duwi synclines are asymmetrical, with gently dipping eastern and northeastern limbs and steeper western to southwestern limbs. The eastern limbs show a progressive decrease in dip toward the west, moving away from the influence of the Nakheil fault.

3. Stratigraphy

The Late Oligocene to Early Miocene basin-fill sequence of the Duwi Basin consists of siliciclastic alluvial deposits and lacustrine carbonates exposed along the basin margins (Figure 1). The lithostratigraphy of the basin-fill sequence has been thoroughly investigated in several studies [11,12,14,22,23]. The Late Oligocene–Early Miocene basin-fill succession was identified and divided into three synchronous rock units, the Nakheil, Abu Ghusun, and Sodmin formations [24]. The age of these formations is estimated to be between 21 and 24 Ma, based on previous studies [11,24,25,26]. This study focuses on the early syn-rift basin-fill succession, which is represented by the Sodmin Formation and is particularly well-exposed in the western margin of the basin along the Duwi fault block (Figure 1). Taking into account the vertical and lateral lithological variations, the sequence of the Sodmin Formation is subdivided stratigraphically into two informal units: Units 1 and 2 (Figure 2).

3.1. Unit 1

This unit unconformably overlies the prerift Thebes Formation. It is highly tilted and reaches a maximum thickness of up to 40 m. The lower part consists of a thin layer of breccias and conglomerates, which transition upward into gray to grayish-white, highly indurated ledges of desiccated micritic limestone. These deposits grade vertically into brecciated and nodular limestone beds exhibiting cyclic bedding patterns. Upward, the micritic limestone beds thin, while the nodular and brecciated limestones thicken. The bed contacts are either sharply planar or undulating, with erosive bases. The upper part is dominated by mixed rootlet, nodular, and brecciated limestone, interbedded with fine-grained siliciclastic beds (mudstone and siltstone). The unit terminates with mottled limestone and massive to laminated calcretes. To the south, the lacustrine carbonates pinch out, forming tongues of stromatolitic limestone within channelized sandstones and conglomerates of the equivalent Nakheil Formation.

3.2. Unit 2

Unit 2 is divided into two distinct parts separated by a karstified surface (up to 20 m thick). The lower part displays a dark brown color and is primarily composed of algal-laminated dolomites containing stratified chert nodules and lenses. Each dolomite bed is capped by intra-paleokarst surfaces and calcrete deposits. These sediments frequently exhibit unconformities and slumping structures. The upper part dips eastward, onlapping and truncating the lower part. It consists of yellow to brown, thin-bedded, massive dolomites interbedded with reddish-brown paleosols, gravels, and sands. Progressing upward, the lithology shifts to algal-laminated and massive dolomites alternating with chert nodules and lenses.

4. Material and Methods

For this study, a total of 100 samples were collected from seven lithostratigraphic sections along the western margin of the Duwi half-graben basin. All hundred samples were prepared as thin sections, stained with Alizarin Red-S, and analyzed petrographically to examine microfacies assemblages, fabric, and composition of lacustrine–palustrine limestones and dolomites, as well as to correlate the spatial distribution of carbonate facies. Chemical analysis of nine selected carbonate samples (four samples of lacustrine and palustrine limestones; five samples from laminated and massive dolomites) was carried out using PAN analytical Axios Advanced X-ray fluorescence spectrometry (XRF) at the central laboratories sector of the Egyptian Mineral Resources Authority (EMRA), Cairo, Egypt. Quantitative measurements of major oxides (CaO, MgO, Fe₂O₃, SiO₂, Al₂O₃) and loss on ignition (LOI), as well as trace elements (Sr, Ba, Na, and K), were achieved (

Table 1. Concentrations of major oxides, trace elements, and molar ratios of CaO/MgO, Sr/Ca, and Mg/Ca in lacustrine carbonates.

Facies	S. No.	Major Oxides and Elements (wt%)								Trace Elements (ppm)
		CaO	MgO	SiO2	Al2O3	Fe2O3	LOI	Ca%	Mg%	Na	K	Sr	Ba	Cao/MgO	Sr/Ca	Mg/Ca
Massive dolomites	36 NN	28.16	18.49	2.3	0.13	1.29	49.54	20.1	11.09	148.4	207.4	560	29	1.52	0.0013	0.92
	35 NN	30.51	20.27	0.88	0.15	1.06	46.99	21.8	12.2	111.3	456.4	171	27	1.51	0.00036	0.933
	32 NN	32	19.37	0.95	0.13	0.3	47.12	22.9	11.6	74.2	456.4	800	30	1.65	0.0016	0.844
Laminated dolomites	27 NN	28.79	19.81	4.5	0.23	0.78	45.78	20.6	11.9	74.2	373.4	195	23	1.45	0.00043	0.96
	21 NN	31.5	20.05	1.04	0.09	0.25	46.95	22.5	12.03	74.2	414.9	107	26	1.54	0.00022	0.89
Lacustrine and palustrine limestones	13 N	49.84	0.762	4.16	4.16	0.66	40.35	35.6	0.457	254	23	122	23	65.41	0.00016	0.036
	9 N	48.72	1.16	3.96	4.02	0.16	41.96	34.8	0.696	50	40	125	40	42	0.00016	0.033
	8 N	51.52	0.73	1.18	5.17	0.28	41.11	36.8	0.438	40	16	103	31	70.58	0.00013	0.02
	3 N	50.57	0.43	2.2	3.3	0.3	43.19	36.1	0.258	40	13	105	24	117.6	0.00013	0.012

). Moreover, twelve selected samples of limestones, dolomites, and mud rocks were analyzed by X-ray diffraction (XRD) at X-Ray Centre Laboratories (Sohag University), Sohag, Egypt, using Philips XRD systems, sourced from the Netherlands, operating at 40 kV and 30 mA with monochromatic Cu Kα radiation (λ = 1.54060 Å). These analyses determined the bulk mineralogical composition and the degree of dolomite ordering, as indicated by the measurement of indices 015 and 110 from X-ray traces.

Isotopic analysis (ᵹ¹³C, ᵹ¹⁸O) was performed on 19 carbonate samples to determine geochemical similarities or differences across the carbonate facies and to support environmental interpretations. Carbon and oxygen isotopic compositions (δ¹³C_carb and δ¹⁸O_carb) of carbonate samples were analyzed at Wuhan Sample Solution Analytical Technology Co., Ltd. (Wuhan, China) using the phosphoric acid reaction method with a Gas Bench II system coupled to a DELTA Q isotope ratio mass spectrometer (Thermo Scientific™, Waltham, MA, USA). The standard deviation for repeated measurements ranged from ±0.1‰ to ±0.2‰ for δ¹³C and δ¹⁸O. Approximately 100% phosphoric acid was added to the carbonate samples, and the reaction was carried out in a water bath maintained at a constant temperature of 50 °C under vacuum conditions for 24 h.

The isotopic results (

Table 2. Stable isotope compositions of representative samples of lacustrine *, palustrine ** limestones and calcrtets ***, stromatolitic limestone ****, laminated dolomites ⁺, and massive dolomites ⁺⁺.

Sample No.	Stable Isotopes
	δ18 O	δ13 C
1N *	−7.59	−8.01
3N *	−7.98	−9.44
6N *	−7.89	−10.04
9N **	−7.14	−9.13
8N **	−7.24	−8.89
11N **	−6.77	−8.95
13N **	−7.14	−8.9
15N ***	−6.6	9.21
16N ***	−6.8	−8.4
STR ****	−9	−9.37
21NN +	−8.4	−6.8
27NN +	−1.82	−2.69
32NN +	−3.05	−2.05
35NN +	−2.2	−2.34
25CN +	−3	−1.99
36NN +	−0.68	−2.35
13SN ++	−3.4	−7.73
6M ++	−3.06	−3.55
10CN ++	−6.74	−1.42

) are expressed in per mil (‰) relative to the Vienna Pee Dee Belemnite (VPDB) standard. International and national reference materials used in the analysis included IAEA-603 (δ¹³C = +2.46‰ VPDB, δ¹⁸O = −2.37‰ VPDB), NBS-18 (δ¹³C = −5.01‰ VPDB, δ¹⁸O = −23.2‰ VPDB), GBW04405 (δ¹³C = +0.57‰ VPDB, δ¹⁸O = −8.49‰ VPDB), and GBW04406 (δ¹³C = −10.85‰ VPDB, δ¹⁸O = −12.40‰ VPDB). One standard was analyzed after every five samples to ensure data accuracy and instrument stability. The analytical precision was better than ±0.2‰ (1σ) for both δ¹³C and δ¹⁸O measurements.

5. Results

5.1. Petrology and Sedimentology

The studied carbonate deposits exhibit variable facies that correspond to various depositional environments [22,24]. These environments reflect the shift from distant alluvial fan zones to lake areas (Figure 2 and Figure 3a).

5.1.1. Limestone Facies

The stromatolitic limestone is laterally discontinuous, interbedded with the conglomerates, and well-developed in the southern part of Duwi Basin (Figure 2). Stromatolites can be classified into three morphological types: stratiform, domed, and thin planar structures. These stromatolites are thought to have originated in isolated, shallow ponds that formed during periods of low discharge [24]. The thickness of beds ranges from 0.5 to 1.5 m. In general, irregular, oncoidal, and domal types are common, as shown in their internal structure (Figure 3b). Small-scale brecciation resembling a tepee structure and some desiccation cracks are seen [27]. The domal-like type is found in the growth position (up to 30 cm in height and 45 cm in width) and consists of a series of continuous, vertically convex laminae (Figure 3b).

In thin sections, the stromatolites are distinguished by an alternation of thicker, light-colored microsparite laminae (200 to 500 mµ) intercalated with thinner, dark irregular micritic laminae (20–40 µm, Figure 4a). The dark micritic laminae create severely crinkled convex hemispheres. Algal filaments with internal diameters ranging from 0.06 mm to 0.4 mm are observed growing perpendicular to the laminae. The filaments are broad and preserved as a ghost structure of clear tubular forms with micrite envelopes. No branching was observed. These stromatolites are mostly composed of low-Mg calcite.

The lacustrine–palustrine limestone facies comprise a vertical arrangement from primary lacustrine limestone to pedogenically modified (palustrine) facies. It is arranged in repetitive parasequences, exhibiting a prominent shallowing-upward trend, and includes sedimentary discontinuities (Figure 3c). These parasequences are thicker in its lower part (up to 3 m) compared to its upper part, where cycle thickness ranges from 0.3 to 1 m. The degree of pedogenic modification increases upwards in these parasequences. For example, eight parasequences were identified showing vertical lithofacies variations that gradually pass from primary, biomicrite lacustrine into limestones displaying a broad range of textures from the base to the top: (1) biomicrites and mottled limestones are capped with coarse intraclastic rudstones; (2) fully brecciated desiccated limestones produce a limestone that is entirely composed of relatively “in situ” breccia (Figure 3d). The top of this bed is irregular and orange in color due to the presence of clay and iron oxides. (3) Carbonate mudstones and wackestones with a lacustrine biota (Figure 4b) pass upward into intraclastic and brecciated grainstones (Figure 4c), which are overlain by pedogenically modified limestones with microkarst cavities and abundant root bioturbations (Figure 4c,d). (4) Mottled limestone is capped by granular limestone. (5) Micritic limestone is followed by brecciated and desiccated limestone (Figure 3e). (6) Rootlet limestone is interbedded with siltstone and fine sandstone (Figure 3f). Several characteristics of the discontinuities in these lithofacies include alluvial channels, calcretes, flat pebble breccias, root mats, microkarstified and/or dehydrated limestones, intense dissolving processes, and additional incipient soil development.

5.1.2. Calcrete Facies

In general, calcrete profiles display an upwardly increasing carbonate content at the expense of the host siliciclastic sediments. These profiles range in total thickness from 0.5 to 3 m. The calcrete deposits consist of three main types: nodular, massive, and laminar. The nodular calcretes consist of calcareous nodules of various sizes and shapes scattered within the matrix of the siltstones and sandy mudstone, with sharp boundaries. Morphologically, these nodules range in shape from spherical to irregularly coalesced, forming concretionary calcretes. In some places, the nodular calcrete grades upward to the massive calcrete (Figure 3g). The color of the nodules ranges from white to light gray. Desiccation fissures, mottling, and diffuse margins are visible. Microscopically, the nodular calcrete is represented by micrite nodules embedded in the host sediment matrix. In the nodular type, the authigenic calcite replaces and displaces the muddy and silty matrix, resulting in isolated patches floating in micrite-calcite groundmasses. The massive calcrete (stage III) marks the end of the calcrete profile and varies in color from white to yellowish white [28]. It is generally dense and hard with some chalky varieties, reaching a thickness of up to 1.5 m. In some places, the massive calcrete grades upward to the palustrine limestone. Microscopically, the massive calcretes appear as a mosaic of microsparite calcite (5–12 µm in size), locally stained by manganese oxides. Detrital quartz and rock fragments are observed. The laminar calcrete (Figure 4f) occurs in the palustrine limestone and dolostone facies of the Sodmin Formation and is made up of alternating irregular and discontinuous microsparite and micrite laminae. The various laminae are distinguished by differences in the density of the micritic texture and are typically less than 3 mm thick. Alveolar septal and peloidal textures are common in the laminar calcrete.

5.1.3. Channeled to Distal Alluvial, Siliciclastic Facies

This facies association exhibits lateral variations in thickness, ranging from 20 m in the south to 6 m in the north. Vertically, it shows a gradual color transition from gray at the base to brick red and dark brown, reflecting a shift toward oxidizing conditions and a declining water table. The facies are primarily composed of siltstone, claystone, and fine-grained sandstone, with subordinate channel conglomerates and coarse-grained sandstone. The quartz grains show remarkable solution features (Figure 4g). Calcareous paleosols and mottling are widespread throughout the deposits. Interbedded within the alluvial sediments are white micritic limestones. These carbonates display red mottling and in situ brecciation, suggesting deposition in a palustrine lake setting that later underwent pedogenic modification during intermittent subaerial exposure.

5.1.4. Dolostone Facies

Laminated dolostone facies is the most common facies in the lowermost part of the Sodmin Formation (Figure 5a,b). Towards the south, it occurs as lenticular bodies (0.5–1 m thick) interbedded with conglomerates. Dolomites extend toward the central parts of the basin and are interbedded with chert and mudstone (Figure 2). This dolomite shows lamination to shrub microfabrics. The laminations are locally slumped due to syn-sedimentary tectonism. These dolomite laminae are discontinuous and some layers are lensoid or continuous (1–4 cm thick). They consist of homogeneous and equant dolomite crystal mosaics. Algal mats are extended structures that preserve the original tissue composition (Figure 5c). Under a microscope, the laminated dolostone’s common texture is made up of alternated light and dark layers (Figure 5c).

The light layers consist of a mosaic of unzoned crystals [29]. They are clear rhombohedrons with slightly cloudy cores and clear rims. The laminated dolomite crystals exhibit a unimodal size distribution and coarse-crystalline, varying from 170 μm up to 390 μm in size, and are subhedral to euhedral with planar facies (Figure 5d). The dark layers are composed of dense dolomicrite. Spheroidal dolomite is also observed replacing dolomicrite (Figure 5e). The second microfacies type, also associated with laminar bindstone, consists of dolomite shrubs. These shrubs have a dendritic structure, with branches splaying from a central stem (Figure 5f). Pedogenic features such as rhyzocretions, circular shrinkage cracks, red calcimorphic paleosols, and calcitized dolomite crusts and patches at the tops of the dolomite beds are encountered (Figure 5e,f). Elongated cavities parallel to the bedding are also present. Laminated fenestrae and vuggy structures are also observed (Figure 5g). Large, irregularly shaped voids with drusy calcites that range in diameter from a few centimeters to several decimeters are characteristic of karst-related features, impacting the dolomites at the top (Figure 5h).

The massive dolomites consist of homogeneous beds ranging from 0.5 to 1.5 m thick. Petrographically, the size, shape, and internal structure of the dolomite crystals vary significantly. They range in size from 13.5 μm to 250 μm and in shape from subhedral to anhedral rhombs and occasionally rounded crystals. Accordingly, three dolomite fabrics are recognized: (i) minute crystals of dolomites (dolomicrite, Figure 6a); (ii) microsparitic dolomites; (iii) coarse, zoned dolomites (Figure 6b,c,d); and (iv) rounded dolomites. The dolomite crystals exhibit a broad bimodal size distribution and create a mosaic texture. Sometimes, chert progressively replaces some of the dolomite crystals. Fossils are very scarce. Large voids (up to 1 m in length), rhyzocretions, and laminar calcretes are examples of pedogenic features that are limited to bed tops (Figure 6e). Other pedogenic features, such as large root cavities, irregular dissolution channels, and circular shrinkage cracks, are also observed (Figure 6f,g). These cavities are partially filled with phreatic calcite (Figure 6h).

5.1.5. Chert Facies

Chert facies dominate the uppermost part of the Sodmin Formation. It occurs as nodules, lenses, and beds or other irregular shape accumulations.

The nodular cherts are randomly distributed within the dolomites of the Sodmin Formation. They are translucent and range in color from brown to grey and occasionally blackish (Figure 7a). The nodules are rounded with a diameter of 5 to 10 cm and may display irregular shape. They have sharp boundaries with the surrounding dolomites. The microscopic analyses reveal that the nodules are composed predominantly of cryptocrystalline quartz and amorphous silica (opal).

The lenticular and bedded cherts are also recorded within the dolomite sequence. Lenticular cherts, measuring 15 to 25 cm in length and up to 10 cm in thickness, are thought to represent the transitional stage between nodular and bedded cherts. The long axes of these bodies run parallel to the laminated dolomite fabric and bedding planes (Figure 7b). In most places, the lenticular cherts are located near the top of dolomite beds, and they are occasionally in contact between dolomite parasequences surrounding dolomite host rocks (Figure 7c). Laterally, the shapes of these beds (up to 20 cm) vary from regular and even to uneven and undulating. Occasionally, the formation of bedded cherts may result from the joining of a sequence of silica lenses that are juxtaposed. Sharp contacts characterize the boundaries between the chert bands (Figure 7d,e). Microscopically, the lenticular cherts within laminated dolomites are composed of a rhythmic alternation of dark and light laminae (Figure 7f). The dark laminate is composed of microcrystalline dolomite. The light laminae are thicker and composed of micro to coarse-grained quartz (Figure 7g).

Laminated dolomites, mudstones, and cherts comprise a 5 m thick succession of dark grayish-green laminated siltstones and mudstones interbedded with laminated dolomite (Figure 7h). The algal-laminated dolomite layers range from 0.2 to 0.5 m in thickness. Individual chert layers exhibit significant lateral thickness variations, reaching up to 0.2 m. Black matter is abundant in thin siltstone layers, which are either massive or slightly laminated, containing abundant black organic matter. In some localities, dolomite beds exhibit in situ brecciation.

6. Mineralogy and Geochemistry

6.1. Mineralogy

X-ray analyses of the lacustrine limestones and dolomites indicate that the low-Mg calcite (LMC) mineral is the most abundant in the lacustrine limestone (nearly 95%), followed by quartz with lower amounts (2–5%) (Figure 8a). The major peak reflection of calcite (104) is presented mainly at 29.4° 2θ with d-spacing 3.035 Å, as well as the CaCO₃ mole% value reaching 99.67%. The dolomites are composed mainly of dolomite and a trace quantity of quartz; evaporite minerals are absent (Figure 8b).

According to the mole% CaCO₃ and MgCO₃ values determined in the laminated dolomites (38.0572 to 51.43 mole% CaCO₃), the mole% MgCO₃ values (48.57 to 61.943 mole% MgCO₃) can be characterized as slightly Ca-rich, therefore being near stoichiometric to nonstoichiometric [29,30,31,32], and the dolomite exhibits a moderate to high degree of ordering [33,34]. The massive dolomites display 57.07 to 57.77 mole% CaCO₃ and 42.23 to 42.93 mole% MgCO₃, indicating nonstoichiometric Ca-rich dolomites. The dolomite content interbedded with mudstones and cherts indicated that the dolomite content ranges from 31.9% to 58.5%. Moreover, the smectite was the most abundant clay mineral in the mud rocks (33.3% to 49.1%). Quartz was present in a ratio ranging from 4.2% to 25.8% (Figure 8c).

6.2. Geochemistry

The results of geochemical analysis of the main major oxides, such as CaO, MgO, SiO₂, Al₂O₃, Fe₂O₃, and LOI, for some representative lacustrine and palustrine limestones, as well as the CaO/MgO ratios and the geochemical signals such as Mg/Ca, are presented in Table 1. The CaO content is predominant and ranges from 48.72% to 51.52%. The concentration of MgO ranges from 0.43% to 1.16% and that of SiO₂ from 1.18% to 4.16%. The content of Al₂O₃ ranges from 3.3% to 5.17%. Fe₂O₃ occurs in lower quantities; it ranges from 0.16% to 0.66%. The loss of ignition (LOI) ranges from 40.35% to 43.19%. The CaO/MgO ratio ranges from 42 to 117.6. The Mg/Ca mole ratio varies from 0.012 to 0.036. The correlation between coefficient values and bivariate plots indicates that the CaO content shows a strong negative correlation with that of the MgO and SiO₂ contents (Figure 9a). CaO has a weakly positive correlation with both Fe₂O₃ and Al₂O₃ (Figure 9b). The MgO content has a moderate to weakly positive correlation with SiO₂ and Al₂O₃, respectively (Figure 9c). SiO₂ and Fe₂O₃ have a weak positive correlation, while SiO₂ and Al₂O₃ show a weak negative correlation (Figure 9d).

In the laminated dolomites, the CaO content ranges from 23.69% to 31.5%. The content of MgO ranges from 17.28% to 20.05%. The SiO₂ content ranges from 0.55% to 9.64%. Al₂O₃ occurs in lower quantities; it ranges from 0.06% to 0.23%. Fe₂O₃ ranges between 0.25% and 2.58%. The loss of ignition (LOI) has high values and ranges from 45.78% to 49.35%. In the massive dolomites, the CaO content ranges from 28.16% to 32%. The MgO content ranges from 18.49% to 20.27%. The SiO₂ content ranges from 0.88% to 2.3%. Al₂O₃ ranges from 0.13% to 0.15%. Fe₂O₃ ranges between 0.3% and 1.29%. The loss of ignition (LOI) has high values and ranges from 46.99% to 49.54%. The Mg/Ca mole values range from 0.844 to 0.933 mole. The MgO content displays strong positive correlations with CaO and Fe₂O₃ contents (R ranging from 0.87 to 1.0) (Figure 9e–f) and strong (R = −0.86) to moderate (R = −0.31) negative correlations with SiO₂ and Al₂O₃, respectively (Figure 9g–h).

For cherty dolomite, the CaO content ranges from 5.35% to 20.26%. The MgO content ranges from 8.28% to 15.5%. There is a high percentage of SiO₂ content ranging from 17.91% to 57.6%. Al₂O₃ ranges from 0.15% to 0.42%. Fe₂O₃ ranges between 1.15% and 2.11%. For alkalis, Na₂O content equals 0.04%, and the K₂O content ranges from 0.04% to 0.07%. The loss of ignition (LOI) ranges from 26.4% to 44.65%. In the nodular chert, the percentage of SiO₂ content is up to 81.27%. Al₂O₃ content equals 1.58%. Fe₂O₃ content equals 4.33%. Na₂O content equals 0.06%, and the K₂O content reaches 0.09%. The loss of ignition (LOI) is low (10.64%).

Na, K, Ba, and Sr were chosen for analysis due to their significance in diagenesis and carbonate precipitation. In the lacustrine and palustrine limestones, the Na content ranges between 40 and 245 ppm. The content of K ranges from 13 to 40 ppm. The concentration of Sr ranges from 103 to 125 ppm. Ba content varies from 20 ppm to 39 ppm. In the laminated dolomites, the concentration of Na ranges from 74.2 to 148.4 ppm. The K content ranges from 166 ppm to 414.9 ppm. The massive dolomites exhibit Sr ranging from 171 to 800 ppm. Ba content varies from 23 ppm to 30 ppm. The Na content ranges from 74.2 to 148.4 ppm. The content of K ranges from 207.4 ppm to 456.4 ppm. In the limestone palustrine facies, there is a very strong negative correlation between Ca% and Sr (Figure 10a). The Ca% with K and Na also show a negative correlation (R = 0.79 and 0.05). The Mg content has a weak negative correlation with Na% and a positive correlation with K and Sr% (Figure 10a,b). In the dolomite facies, Na (ppm) shows a moderate negative correlation with Mg% and Ca% (R =−0.20 and 0.27). K (ppm) content weakly correlates with Ca% and Mg% (R = 0.16 and 0.13) (Figure 10c–f).

6.3. Isotopic Analysis

Results of δ¹⁸O and δ¹³C isotopes are presented in Table 2. The oxygen isotope (δ¹⁸O) values of the lacustrine facies are variable, ranging from −10.03‰ to −9.13‰, whereas δ¹³C values are ranging from −7.98‰ to −7.14‰. Calcrete samples have values of δ¹⁸O that range from −9.21 ‰ to −8.40‰, and δ¹⁸C values vary from −6.80‰ to −6.60‰. Laminated dolomite samples have variable values of δ¹⁸O ranging from −3.40 to −1.55, whereas δ¹⁸C values vary from −3.55‰ to −2.05‰. In the massive dolomites, the δ¹⁸C and δ¹⁸O values range from −2.34‰ to −1.99‰ and −3.00‰ to −2.20‰, respectively. In general, dolomite interbedded with silica and mud rocks has a more depleted ¹⁸O isotope value (−6.74‰) than massive and laminated dolomite (−2.20). A cross-plot of the isotopic values for several carbonate deposits has been created using the δ¹⁸O and δ¹³C diagrams (Figure 11).

7. Discussion

7.1. Geochemical Discrimination of Depositional Environment

The XRD bulk mineralogy of the lacustrine and mixed palustrine limestone and calcrete facies is dominated by low-Mg calcite (LMC). Generally, higher CaO relative to MgO values indicates that calcite is the predominant mineral and that dolomitization did not occur during this deposition phase. These data also document the presence of organism-generated low-Mg calcite, consistent with dominant calcite composition [2,35]. Furthermore, the Ca/Mg ratio tends to become higher when gastropods and ostracods are present, and this ensures the low salinity of lake water during limestone precipitation. The soil infilling pseudo-karst cavities and root traces in these limestones is rich in clay and silt, possibly contributing to the relative increase in SiO₂ and Al₂O₃ content [12]. Terrigenous influx, associated with iron-bearing solutions, may explain the observed variation in Fe₂O₃ concentrations [36]. Loss on ignition (LOI) values ranging from 40.35% to 43.19% likely reflect high volatile and carbonate contents, corresponding to increased CO₂ release upon heating to 1000 °C [37]. The Mg/Ca ratio in the limestones ranges from 0.012 to 0.036, while Sr/Ca and Mg/Ca ratios vary from 0.00013 to 0.00016, which fall within the range reported for carbonate lakes [2,38], confirming deposition in low-salinity lacustrine environments. Regarding the bivariate plots, the significant inverse relationship between CaO% and SiO₂% suggests that there is no genetic relationship between these two oxides. It may also mean that certain amounts of quartz remained insoluble, which could be related to the influx of detrital quartz during deposition. Furthermore, the MgO percentage rises as solutions leach CaO, as indicated by the significant negative correlation between MgO% and CaO% [39].

The bivariate plot of Sr (ppm) and Ca% shows a strong negative correlation, and this may indicate the substitution of Ca²⁺ by Sr²⁺ within calcite lattices [40]. The lower values of Sr and Ba in the lacustrine limestones indicate a continental origin for the lake water and vadose meteoric waters enriched the lacustrine limestones [41,42]. Furthermore, the depletion of K and Na contents in the palustrine limestones confirms extensive paleopedogenic modifications consistent with the periodic lake level fluctuations. Additionally, the strong negative correlation between Ca% and K indicates the low input of K-feldspar minerals during the precipitation.

The dolomites facies displayed CaO/MgO ratios between 1.65 and 1.54, which is extremely similar to the mineral dolomite. The Sr/Ca ratio varies from 0.00022 to 0.0016, and the Mg/Ca ratio ranges from 0.8444 to 0.96. The Mg/Ca ratio is similar to those of lacustrine dolomite in the Bohai Bay Basin in east China [43]. These values clearly demonstrate that the studied dolomites were formed from saline lake waters. The low CaO/MgO ratios support high-Mg dolomitic content and are consistent with the non-stoichiometric nature [30,44,45]. In some laminated dolomites samples, the Mg/Ca molar ratio tends to increase. This possibly reflects enrichment by Mg-rich clays derived from clay minerals. Additionally, compared to samples of laminated dolomite in hypersaline evaporative conditions (~900 ppm) [40,46], the concentration of Sr in the laminated samples (107–195 ppm) is lower. This depletion may be due to the influence of meteoric water during the early stage of diagenesis when the dolomites were crystallizing [40,46]. The negative correlations between MgO and SiO₂/Al₂O₃ observed in the bivariate plots and correlation coefficients (Figure 9g–h) suggest that aluminosilicates remained as insoluble fractions, possibly due to detrital influx during deposition.

Furthermore, because of the meteoric fluids, several samples included coarsely crystalline dolomite, indicating subsequent diagenetic activity [47]. The presence of calcitized dolomite textures supports the impact of fresher water throughout developing lacustrine cycles. This suggests that the arid paleoclimate alternated with humid seasons during the development of the dolomite. Large rhizocretions and red dolomite beds with calcic paleosol intervals at the tops of the laminated dolomites may be signs of ongoing subaerial exposure. The high Sr concentration (560–800 ppm) in some dolomite samples indicates that saline conditions persisted during the microbial dolomite’s production and/or enrichment with Mg from terrigenous input. Dolomite crystals that are bimodal are present, which supports this hypothesis. Furthermore, the laminated dolomites are ordered and nearly stoichiometric to non-stoichiometric, suggesting a high level of dolomitization of algal laminates [48,49] and their formation under arid climate conditions [20]. Other studies suggest that hypersaline dolomites formed in ambient fluids with high Mg/Ca ratios tend to be more stoichiometric [44,45,46,50] and reflect the rapid crystallization of dolomite in a penecontemporaneous evaporation [51]. Such a higher Mg/Ca ratio indicates that the saline conditions were maintained during the formation of dolomite.

The results of isotopic values indicate that the carbonates are arranged in two major groups, most probably reflecting different paleoenvironmental conditions during carbonate precipitation. Lacustrine and palustrine limestones exhibit the highest negative values, comparable to calcretes (Figure 11). This indicates the close relationship between the carbonate types and the paleo-hydrologic environments in which they were deposited. In comparison, dolomites exhibit significantly fewer negative δ¹³C and δ¹⁸O values. Additionally, the different δ¹⁸O values of dolomite, palustrine limestone, and calcrete indicate that these two carbonate types developed in sedimentary sub environments with different hydrochemistry. In this context, strongly negative (up to −10.03‰) δ¹⁸O values found in the palustrine limestones would suggest the input of isotopically light waters of meteoric origin in a hydrologically open lake [52], which is consistent with pedogenic features linked to subaerial exposure and lake margin fluctuations [16], and they correlate well with the oxygen composition of palustrine limestone of the Rupelo Formation, west Cameros Basin [16]. This hypothesis is supported by the low Sr concentrations found in the carbonates. Additionally, the δ¹⁸O values in the palustrine limestone facies are generally higher (δ¹⁸O = −8.89‰), relative to those of the underlying lacustrine carbonates (δ¹⁸O = −10.03‰). A similar pattern is observed in the dolomite facies, where the δ¹⁸O values in the laminated dolostones reach as low as −3.05‰, whereas in the massive dolomites near the top, values increase to −0.68‰. This variation suggests an evolution of the waters toward more evaporative conditions under an arid climate, resulting in an enrichment in δ¹⁸O values of the precipitated limestones and dolomites, which is in good agreement with the upward increase in evidence for pedogenic features associated with subaerial exposure and fluctuations of the lake margin. The overall negative δ¹³C values of both lacustrine, palustrine, and calcrete facies (−6.60‰ to −7.98‰) could indicate that biological effects associated with root activity have enriched isotopically light carbon [53,54,55,56], in addition to the HCO₃ source coming from meteoric water that is drained from the nearby groundwater [54]. Sample 13SN, with a relatively high negative δ¹³C value (−7.73‰), may suggest the palustrine setting of the dolomite beds was strongly affected by rhizocretions and root molds. Similarly, the relatively negative δ¹³C values found for the lake margin dolostone suggest a contribution from plants. The lighter isotope of oxygen and carbon values (at −9.37‰ and −9.0‰, respectively) in algal stromatolites may suggest formation in humid freshwater environments [57], possibly due to river input from nearby carbonates (Thebes Formation). Similar isotopic values for carbon and oxygen were reported from mid-Cretaceous lacustrine stromatolites in the Gyeongsang Basin of South Korea [57].

7.2. Sources and Mechanisms of Dolomite and Chert Formation

7.2.1. Biogenic Formation Mechanism

In general, biogenic (microbially mediated) dolomite and chert formation through microbial activity has been well-documented elsewhere in other locations [7,58,59,60,61,62,63,64,65,66,67]. The following is a suggested microbial dolomite and chert precipitation mechanism that can be applied to interpret laminated dolomites and related cherts. The algal mats and the cyanobacteria tend to grow in lake margin environments, where the water is frequently affected by desiccation episodes. Under such conditions, the high Mg/Ca ratio and the formation of dolomite are provided by the magnesium accumulated in the laminated and stromatolitic cyanobacteria through their growth, particularly during the late evaporation stage [61]. Additionally, under these conditions, silica-bearing material is more easily dissolved by alkaline water compositions, leading to elevated concentrations of aqueous silica. Subsequently, the increase in CO₂ that results from the decomposition of organic matter lowers the pH value [68,69].

The decomposition of organic matter, primarily driven by algal mortality, increases CO₂ levels, which lowers the pH [68,69]. Organic-rich materials, resulting from the algal mortality, are the main source of CO₂ [70]. The prevalence of laminated fenestral structures in these facies supports the release of CO₂ and the decomposition of organic materials (Figure 6e,f), leading to significant silica supersaturation and precipitation of nodular chert (Figure 6g,h). The existence of lenticular and nodular cherts within the algal-laminated dolomite facies is consistent with this mechanism. In general, this mechanism of dolomite and chert precipitation aligns with that described for dolomite–silica facies in Miocene lacustrine carbonates from Madrid and Duero Basins, Spain [7,71,72]. In the study area, further evidence supports this biogenic mechanism. The preservation of the original rock structure, such as the stromatolitic and algal laminate fabrics in dolomite, provides evidence of microbial origin [73] and non-replaceable relationships between dolomite and silica developed from microbial mats. The prevalence of the laminated fenestral and bird-eye and vug structure supports the realization of magnesium and the decomposition of organic materials. In addition, there are contributions from Mg-derived microbial activity sources, as evidenced by the presence of spheroidal dolomite crystals which are poorly ordered and nonstoichiometric [74]. The well-preserved micro-lamination and shrub fabrics in the mats’ microstructure are evidence of microbial-mediated processes [7,75]. On the other hand, the existence of microbial film remnants in the laminated dolomite can explain the presence of silica, as such films provide a location for silica precipitation. This biological origin is further evidenced by the dolomite’s isotopic signature; its significant enrichment in ¹³C indicates that organically derived carbonate was incorporated during its formation [76].

7.2.2. Abiogenic Formation Mechanism

This mechanism seems plausible for massive dolomites and lenticular/banded cherts in the marginal and basinal lake settings. Regarding the sources of silica and magnesium, it is believed that the silica is derived from the surrounding pre-rift Thebes and Duwi formations, which are mainly composed of cherty carbonate rocks. Also, the magnesium is sourced from terrigenous input (clay minerals) of the uplifted pre-rift upper Cretaceous Dakhla and Duwi formations (which consist of Al-rich clays) [77]. In this context, the alluvial siliciclastics of Units 1 and 2 contain detrital quartz and chert clasts, as well as siltstones and claystones, which represent another potential Si and Mg source. Detrital quartz, in particular, is a well-documented contributor of silica [78,79,80,81,82]. The Si is likely derived from siltstones and claystones, where it was released through diagenetic processes, particularly during the transformation of clay minerals. For instance, it has been suggested that the conversion of montmorillonite to illite releases Si, Mg, and Ca [76,83]. The liberated silica likely entered the lake via groundwater (having a high pH), either in solution or as colloids rather than as detrital grains.

The proposed abiotic dolomite precipitation model is as follows: the lake was filled by alkaline-saline water of a low sulphate concentration. Terrigenous input (clay minerals), primarily sourced from the uplifted pre-rift upper Cretaceous Thebes, Dakhla, and Duwi formations (which consist of Al-rich clays) [77], entered into the Duwi Lake. As a result, Al-rich detrital clays (kaolinite, which is unstable in alkaline lacustrine conditions [84]) were found in the alkaline lake water. Due to the instability of Al-rich kaolinite in the alkaline water, the Al₂O₃ ratio decreased in comparison to MgO. This resulted in the formation of authigenic smectite [85,86,87,88,89,90,91].

In lake waters with high pH values, smectitic clays may neoform as a gel-like, extremely viscous medium [6,91,92,93,94,95]. As a result of increased evaporation brought on by the dryness, the Mg-rich clays (smectite) broke down and may have released significant amounts of magnesium into lake waters, which in turn lowered kinetic barriers for the abiogenic formation of primary dolomite. This mechanism is comparable to the abiotic dolomite model that has been supported by some studies [96,97,98,99,100,101], and it is clearly applicable to the dolomites of Duwi Lake. Also, under these conditions, silica material was more easily dissolved by alkaline waters, resulting in significant volumes of aqueous silica. Following a change toward more humid conditions, alkalinity dropped as a result of the entry of groundwater with a relatively low pH (>9). Consequently, as a result, silica became supersaturated and precipitated abiogenically [98]. This hypothesis is consistent with studies on Permian cherts [9], which demonstrate that the ratio of freshwater input to evaporation controls the pH of these alkaline lakes, and it is obviously applicable to the chert accumulated in marginal and basinal environments.

The abiogenic origin of the Duwi cherts has been supported by several characteristics. In the marginal setting, cherts are close to the top of the dolomite beds and occur sporadically along the discontinuities between the dolomite cycles (Figure 2 and Figure 6c). This points to a genetic connection with the final parts of the regressive sequences, where lakes change from shallow to palustrine environments, facilitating silica precipitation due to water-level fluctuations [2,8]. Additionally, the existence of palustrine environmental characteristics, including rhizocretions and pseudo-karst cavities, which are diagnostic of subaerial exposure episodes and meteoric waters, indicates the lake was intermittently subject to modification by pedogenesis [93]. The presence of replacement markers, including precursor dolomite relics within the lenticular cherts, also supports the early diagenetic origin of chert formation. This is evidenced by elevated CaO (5.35%) and MgO (8.25%) contents in some chert samples, as well as the distally interbedded dolomites with mud rocks and cherts in basinal environments. The alternating layers of cherts, dolomites, and mudrocks suggest cyclic precipitation, likely driven by periodic pH fluctuations. These cherts are analogues to Permian abiogenic chert from northern Italy [9]. Furthermore, the X-ray diffraction of siltstones and mudstones in Unit 1 as well as mudrock-interbedded dolomite and cherts in Unit 2 revealed a high proportion of dolomite minerals with sharp diffraction peaks in the samples (Figure 8). These results suggest that clay precursors provided a significant source of Mg during dolomitization. Additionally, the negative correlation between MgO and Al₂O₃ may reflect the formation of Mg-rich smectite, likely related to the terrigenous input of Al-rich kaolinite from the Dakhla Formation. This could be interpreted by the instability of kaolinite in the alkaline medium and its neoformation into smectite (Mg-rich clay).

7.3. Major Controls: Tectonics, Climate, and Source Rocks

Climate or tectonic subsidence changes are the main controls that influence basin morphology [102,103,104], as well as the evolution of the lacustrine system, potentially altering its stage throughout time [105]. Additionally, source rock should be considered, as it may affect the groundwater chemistry and the types of sediments that accumulate in the lake basin [17,103]. Recently, conceptual frameworks have clarified the influence of tectonics and climate on the lithologies and architecture of lake basin fills [106,107]. These authors believe that the most important factor in identifying the primary characteristics of both recent and ancient basin fills is the relative balance of accommodation rates (primarily controlled by tectonics) with water supply and sediment (primarily controlled by climate). Furthermore, the lake basin stratigraphy responds to tectonic subsidence, particularly in extensional, low-water-budget lacustrine rift basins [107]. The Duwi Basin is in good agreement with [107], Strecker et al. (1999, who found that the basin’s sedimentary fill, which was primarily composed of shallow lacustrine carbonates, developed in an extensional tectonic system. The Duwi Basin is in good agreement with these findings, as its sedimentary fill, dominated by shallow lacustrine carbonates, developed within an extensional tectonic system.

7.3.1. Tectonics

The extensional tectonic regime linked to the NW Red Sea rifting during the Late Oligocene is responsible for the overall structural situation of the Duwi Basin. This tectonic context shaped the basin’s morphology, which at the time evolved from hanging wall synclinal to a half-graben geometry, bordered to the east by the Nakheil Fault segments [13,14,21]. The lacustrine carbonate sequence of the Sodmin Formation, which filled the Duwi lake basin, comprises two units. The tectonic arrangement and stages of the original syn-rift are described in each unit. These correspond to different water level conditions in the paleolake system and are intimately linked to the evolution of carbonate in the sub environments as well as the surrounding relief over time. Two major stages of lake evolution represented by these units.

During stage I, the segmented normal faults of the Nakheil Fault Zone were buried, and the basin was a hanging-wall synclinal depocenter surrounded by a low relief surrounding carbonate-dominated rocks of the Thebes Formation (Figure 12a). This source rock produced calcium-rich carbonate solutions that deposited lacustrine carbonates, dominated by low-Mg calcite, in the basin’s lake systems. These deposits were characterized by fully superimposed cycles during high lake levels, when sediment supply exceeded the accommodation creation, leading to the development of overfilled lake basins [106]. The predominance of palustrine lithofacies that terminate this sequence may document periods of reduced accommodation space, typical of nearly overfilled basins [19]. The overfilled nature of the lake basin has been demonstrated by evidence from stratal architecture, including growth strata patterns and the convergence and onlapping of beds towards the western-dipping limb, away from the syncline axis. Toward the end of this stage, the southern margin of the basin underwent regional reactivation of normal faulting. This tectonic activity was accompanied by the deposition of alluvial fans and braided channels along the southwestern basin margin (represented by the Nakheil Formation), which transitioned northwestward into finer terrigenous alluvial/floodplain deposits and cyclic palustrine limestones and mudstones (the Sodmin Formation). A subsequent regional lake-level drop led to regression, resulting in the development of calcretes and paleosol horizons in the upper portion of Unit 1.

During stage II, the eastern margin of the basin underwent regional reactivation of normal faulting. This activity led to the linkage of the Nakheil Fault Zone, which breached the surface and formed a half-graben basin (Figure 12b). As a result, a shallow, ephemeral, saline, and underfilled lacustrine system developed [105], depositing evaporitic facies (Unit 2). Concurrently, the vertical propagation of faults introduced new source rocks (Upper Cretaceous–Paleocene rocks). This provided the Mg and Si for dolomitization and silicification and nutrients for the microbes. The tectonic reactivation along the eastern basin margin triggered an abrupt shift in environmental conditions, marked by the transition from limestone to dolomite units and the progradation of coarse alluvial deposits over the lacustrine limestones. The upward increase in pedogenic features throughout the sequence, along with evidence of prolonged subaerial exposure, including large rhizocretions, laminar calcretes, pseudo-karstification, and calcimorphic soils, support this activation.

7.3.2. Climate

During the deposition of Unit 1, a humid paleoclimate increased precipitation and surface runoff, which enhanced chemical weathering. This led to lacustrine expansion at a highstand and the development of overfilled and balanced-fill lakes [105]. Freshwater, terrigenous inputs (e.g., Al and Si), and carbonate elements (e.g., Ca, and HCO₃₋) entered the lake basin, resulting in a decrease in water salinity [108]. Evidence for the influence of a humid climate and fresh water conditions was supported by the palustrine limestone’s sedimentary characteristics, such as pseudo-karst cavities, nodularization, rhizobrecciation, and mottling [17,109,110], and fluctuations in the lake water table [111].

The geochemical and stable isotope analyses support the freshwater conditions. The very low Sr/Ca and Na/Ca ratios, combined with the negative isotopic values of both δ¹³C and δ¹⁸O of carbonates of Unit 1, are consistent with lake water that is freshwater and continental in origin and from a hydrologically open lake [52,112]. Freshwater environments are clearly suggested by the assemblage of gastropods (Planorbis and Lymnaea sp. etc.) found in the limestones of Unit 1. Moreover, the low variations in δ¹⁸O indicate low evaporation relative to inflow, which is also compatible with a relatively humid climate. The occurrence of distal alluvial floodplains suggests prolonged wet periods and a humid climate [113]. However, the presence of calcrete horizons interbedded with fluvial deposits in the upper section of Unit 1 points to intermittent arid conditions [19,109].

Under arid climatic conditions, during the deposition of Unit 2, the evaporation rate of the lake exceeded the inflow, resulting in lacustrine contraction and a lowstand. As a result, the pH and salinity of the lake water increased, microbial activity increased, and laminated dolomite and silicification occurred. Additionally, with increased concentrations of Mg and Si, massive, bedded dolomite and chert were formed (at the marginal lacustrine). The interbedded dolomite, mudstone, and chert (in the basinal lacustrine, Figure 12b) resulted from cyclical climate fluctuations between arid and short periods of humid conditions. During arid phases, the lake contracted into a shallow, low-energy, high-salinity lowstand body, facilitating dolomite and chert formation. In contrast, humid climates expanded the lake and favored the deposition of mudstone.

In general, these sediments exhibit signs of aridity and resemble palustrine deposits that are attributed to semi-arid to arid climates [16,17]. However these sediments contain some evidence of subaerial exposure, such as calcimorphic soil, laminar calcretes, pseudokarstification, and large rhyzocretions near the tops of dolomite strata, suggesting long periods of wet conditions alternating with aridity [16,17]. The presence of aeolian sands and the deeply incised channel conglomerates embedded in the dolomites support the assertion. Additionally, depleted δ¹⁸O signatures in dolomites support wet conditions that alternated with the prevailing aridity.

7.3.3. Source Rocks (Provenance)

In the study area, a variety of Cenozoic–Mesozoic formations along the basin borders promoted mixed clastic-carbonate deposition in the lakes during the Late Oligocene and Early Miocene. During the initial stage of basin fill (Unit 1), carbonates were sourced from outcropping Early Eocene Thebes Formation strata. This documents the early low relief of basin margins, which was associated with the formation of synclinal basin geometry at that time. Extensive dissolution of the surrounding highland limestone rocks was derived from surficial and groundwater enrichment of the basin by Ca²⁺ and HCO₃₋, as proven by the widespread occurrence of paleokarstic features [114]. Other evidence supporting their derivation from the nearby late pre-rift rocks is the predominance of coarse-grained (cobbles and boulders) debris flow and stream-dominated sediments. Furthermore, the dominance of clay-poor conglomerates suggests that source area lithologies were largely deficient in clay.

During the second stage, a progressive uplift of the catchment areas of the Duwi Basin due to fault propagation resulted in the emplacing of new source rocks. This led to the unroofing and extensive weathering and leaching of the Upper Cretaceous/Paleocene fine siliciclastic/carbonate rocks, which are stratigraphically older. This is evidenced by the dominance of fine siliciclastics within Unit 2 and the widespread early diagenetic dolomitization and silicification processes of abiogenic origin.

8. Conclusions

• The early syn-rift continental deposits of the Sodmin Formation (Upper Oligocene–Lower Miocene) in the Duwi Basin comprise two units (Units 1 and 2). Unit 1 is dominated by mixed lacustrine and palustrine limestone deposits exhibiting superimposed regressive cycles. This unit is terminated by mixed fine siliciclastics and palustrine limestone. Unit 2 comprises cherts and dolomites interrupted by coarse siliciclastics.
• The studied Sodmin Formation exhibits variable facies that correspond to deposition in a fluvio-lacustrine environment. These facies are as follows: stromatlitic limestone, lacustrine–palustrine limestone, calcrete, channels and distal floodplains, dolomite, and chert.
• Analysis of the lacustrine carbonate facies using petrographical, geochemical, mineralogical, and stable carbon and oxygen isotopes clearly reflects the vertical changes in the paleoenvironments and the lake water chemistry. It demonstrates an abrupt shift from an open freshwater lake condition (Unit 1) to closed saline-alkaline waters (Unit 2) and is consistent with the presence of dolomites and cherts in Unit 2 and their rarity in Unit 1.
• The vertical variations developed in the lacustrine environment reveal the effects of tectonic events (growth faults) and provenance evolution, as well as a tendency towards aridity in the climate. Tectonic activity, particularly the development of hanging-wall syncline folds associated with the propagation of buried normal faults, followed by fault linkage and the establishment of a half-graben basin, influenced the overall architectural evolution of the lake basin. The climate changes indicate that the lower part of Unit 1 was deposited under predominantly humid climatic conditions, while the upper part of this unit suggests alternating periods of humidity and aridity. During Unit 2 formation, greater aridity favored the deposition of evaporitic facies. The provenance data show that Unit 1 was sourced from Eocene pre-rift carbonate sedimentary rocks, whereas Unit 2 was derived from pre-rift Mesozoic rocks with a mixed clastic-carbonate composition.
• Two proposed mechanisms exist for the dolomitization and silicification stages of Unit 2 in the Duwi Basin. The first is microbial (biogenic origin), produced by the dissolution of algal mortality, whereas the non-microbial (abiogenic origin) mechanism is formed by pH oscillations in an alkaline lake environment during the early diagenesis. This can be explained by the fact that alkaline environments provide suitable chemical conditions for the development of microbial mats and precipitation of magnesium carbonates, as well as the dissolution of silicate minerals, which leads to the creation of fluids that were extremely rich in silica.