Nitrate Source and Transformation in Groundwater under Urban and Agricultural Arid Environment in the Southeastern Nile Delta, Egypt

: With the intensiﬁcation of human activities, nitrate pollutants in groundwater are receiving increasing attention worldwide. Especially in the arid Nile Delta of Egypt, groundwater is one of the most valuable water resources in the region. Identifying the source of nitrate in groundwater with strong human disturbances is important to effective water resource management. This paper examined the stable isotopes ( δ 15 N/ δ 18 O-NO 3 and δ 2 H/ δ 18 O-H 2 O) and the hydrogeochemical parameters of the shallow groundwaters in the arid southeast of the Nile Delta to assess the potential sources and transformation processes of nitrate under severe urban and agricultural activities. The results revealed that the groundwaters were recharged by the Nile River. Meanwhile, the inﬁltration of irrigation water occurred in the west, while the mixing with the deep groundwater occurred in the east regions of the study area. The TDS, SO 42 − , NO 3 − , and Mn 2+ concentrations of groundwaters (n = 55) exceeded the WHO permissible limit with 34.6%, 23.6%, 23.6%, and 65.5%, respectively. The NO 3 − concentrations in the shallow groundwaters ranged from 0.42 mg/L to 652 mg/L, and the higher levels were observed in the middle region of the study area where the unconﬁned condition prevailed. It extended to the deep groundwater and eastward of the study area in the groundwater ﬂow direction. The δ 15 N-NO 3 and δ 18 O-NO 3 values suggested that the groundwater NO 3 − in the west and east regions of semi-conﬁned condition were largely from the nitriﬁcation of soil organic nitrogen (SON) and chemical fertilizer (CF). In contrast, wastewater input (e.g., domestic sewage and unlined drains) and prevalent denitriﬁcation were identiﬁed in the middle region. The denitriﬁcation might be tightly coupled with the biogeochemical cycling of manganese. This study provides the ﬁrst report on the groundwater NO 3 − dynamics in the Nile Delta, which generated valuable clues for effective water resource management in the arid region.

To effectively manage NO 3 − pollution in groundwaters, a comprehensive understanding of its sources and transformation processes is necessary.While NO 3 − stems from various sources, including agricultural practices, wastewater, organic matter in the soil, atmospheric nitrogen deposition [24][25][26], and complex transformation processes such as denitrification and nitrification [27][28][29] make it more difficult to determine the exact source of nitrate.The use of isotopic tracer techniques, particularly dual NO 3 − stable isotopes, has been widely employed in various areas to investigate NO 3 − sources and transformations based on the distinct isotopic compositions of NO 3 − sources and the predictable isotopic fractionations [22,[30][31][32][33][34][35][36][37][38].For instance, studies have utilized the dual NO 3 − isotopes to explore the relationship between NO 3 − contamination in groundwaters and agricultural practices [39] and urban activities [30].
Despite the widespread use of this approach, uncertainties can arise when attempting to identify NO 3 − sources [40][41][42].First, isotopic compositions of NO 3 − arising from various sources can exhibit some degree of overlap [38].Second, the isotope fractionation process may obscure the initial isotopic compositions [38].Therefore, other isotopes (e.g., δ 2 H/δ 18 O-H 2 O and δ 11 B), water chemistry (e.g., Cl − and SO 4 2− ), and hydrogeochemical parameters were jointly applied to enhance the accuracy of NO 3 − source identification [22,[43][44][45][46][47][48].The integration of these additional data sets is expected to provide valuable and definitive insights into both water and NO 3 − cycling dynamics.In the arid Nile Delta, the groundwater is a valuable resource because people rely on it for different purposes.The growing population, rapid urbanization, and increased usage of chemical fertilizers have led to severe NO 3 − pollution in the groundwaters.The authors of [49] highlighted significant urban expansion in the Nile Delta region from 1987 to 2015.It is presumed that this expansion has led to an increase in the discharge of untreated wastewater into water bodies.Furthermore, the two main wastewater unlined drains (Belbies and Kalyobiya) cross the study areas.These pollutants will inevitably infiltrate into the groundwater.High NO 3 − levels in the groundwaters have been reported (210 mg/L); however, the sources of pollution have not yet been identified, and the driving mechanisms still remain to be studied.There has been a lack of isotopic studies on NO 3 − pollution in the groundwaters in this region [50,51].This seriously hinders the implementation of groundwater nitrate pollution prevention and control work in the region.
Located at the eastern fringe of the Nile Delta, the studied area is characterized with unlined drainage channels crisscrossing, a wide distribution of illegal shallow wells, and the expansion of urban areas, which further deteriorate the problem of groundwater pollution.In this study, for the first time, we use an integrating approach of a multiple isotope tracer (δ 15 N/δ 18 O-NO 3 and δ 2 H/δ 18 O-H 2 O) combined with hydrogeochemical parameters to identify the sources of NO 3 − contamination and its transportation and transformation processes in the shallow groundwater of this area.The results are expected to provide insights to the effective management of the water resources in the arid region with intense human disturbance.

Study Area
The study area is located in the southeastern Nile Delta, a natural extension of the Nile Delta floodplain stretching toward the east.It extends between longitudes 31  1a).The study area had a population of roughly 12 million people, and the population density was calculated to be 5800 individuals/km 2 [52].The land use is dominated by the interrelation of rural-urban and agricultural lands (Figure S2).The cultivation in the area primarily relies on Nile River water and groundwater for irrigation as a water source.The climate is arid and rainless in summer (May to September), with temperatures ranging from 30 to 40 • C, while the winter season (November to February) is relatively mild, with precipitation ranging from 10 to 20 mm/year and temperatures ranging from 10 to 20 • C. The study area is typically characterized by its flat plains forming the Delta landscape, gently sloping toward the north-northeast and east.It exhibits low elevation and is surrounded by a moderately elevated plateau to the south and southeast (Figure 1b).
Water 2024, 16, x FOR PEER REVIEW 3 of 22 million people, and the population density was calculated to be 5800 individuals/km 2 [52].
The land use is dominated by the interrelation of rural-urban and agricultural lands (Figure S2).The cultivation in the area primarily relies on Nile River water and groundwater for irrigation as a water source.The climate is arid and rainless in summer (May to September), with temperatures ranging from 30 to 40 °C, while the winter season (November to February) is relatively mild, with precipitation ranging from 10 to 20 mm/year and temperatures ranging from 10 to 20 °C.The study area is typically characterized by its flat plains forming the Delta landscape, gently sloping toward the north-northeast and east.It exhibits low elevation and is surrounded by a moderately elevated plateau to the south and southeast (Figure 1b).(b) digital elevation model (DEM) and aquifer thickness; and (c) thickness of the upper semiconfined aquifer layer (modified from [53]) and hydraulic head.(b) digital elevation model (DEM) and aquifer thickness; and (c) thickness of the upper semi-confined aquifer layer (modified from [53]) and hydraulic head.The Quaternary aquifer is semi-confined and consists of two main units, the semi-pervious upper Holocene silt, sand, and silty clay unit (upper Holocene layer) (Figures S1 and S3), with thickness ranging from 0 to 20 m (Figure 1c) [53].It is underlain by unconsolidated Pleistocene sand and gravel with clay lenses, with thickness ranging from a few meters in the south to about 400 m north (Figures 1b and S3).Moreover, the basalt and clay layer underlain the Quaternary aquifer acts as an aquiclude south of the study area, where the aquifer is thin (Figure S4).In contrast, in other areas, the Quaternary is uncomfortably underlain by the Tertiary aquifer, which is hydraulically connected particularly with the pumping increase from the Quaternary aquifer [54,55].The consequences of the high extraction due to the irrigation of the newly reclaimed areas at the southeast corner of the study area create a cone of depression.At the same time, the increase in wastewater and surface water infiltration to the groundwater south of Shibean Elqanater City has increased the water table (Figure 1c).
The groundwater depth was measured in January 2022; it ranges from 2 m to 47 m, with the shallowest levels found near Khanka city and the deepest levels located in newly reclaimed areas southeast of the study area, at well SH35 (Figure 1a).The elevation of the water table fluctuates between 14 and −1 masl, with the highest values observed in the south and southwestern part of the study area, in the Khanka city and its vicinity.The groundwater flow direction exhibits a southwest-to-northeast pattern in the central, southern, and northern regions and a northwest-to-southeast direction in the southeastern part of the study area (Figure 1c).The groundwater recharge primarily occurs through two main sources: Nile River and irrigation canal seepage and infiltration of excess irrigation water, industrial usage, and surface water bodies (e.g., cesspools and drains) [51,56,57].On the other hand, groundwater discharge is mainly attributed to pumping withdrawals for various purposes, such as agricultural irrigation, drinking water supply, and industrial usage.

Sample Collection
A total of 71 samples (16 surface water and 55 shallow groundwater) were collected between December 2022 and January 2023.The surface water samples were collocated as an endmember to represent the potential pollution sources for the shallow groundwater, not for water quality purposes.There are 4 samples from two different wastewater drains (Bilbies and Kalyobiya drains), 2 from Brackish lakes, 2 from agricultural drains, and 8 from surface freshwater.The majority of wells were established for private domestic purposes, with depths ranging from 9 to 43 m below the ground surface, and the average depth is 29.7 m.Each well was pumped 5 to 10 min before sampling to eliminate any stagnant water in the pipes.Of the 55 groundwater samples, 3 were from relatively deep agricultural wells (well depths of more than 50 m), and 52 were from shallow domestic wells.All samples were passed through 0.45 µm cellulose membranes and then collected into pre-washed high-density polyethylene (HDPE) bottles without headspace to avoid evaporation for the analysis of dissolved ions, heavy metals, δ 2 H/δ 18 O-H 2 O, and δ 15 N/δ 18 O-NO 3 .The samples were acidified for major cation and heavy metal analysis by adding a few drops of ultrapure nitric acid to lower the pH below 2 and stored in 60 mL HDPE bottles.Another 125 mL was stored in HDPE bottles for anion, δ 15 N-NO 3 , and δ 18 O-NO 3 analyses.In addition, two 15 mL bottles were prepared for other anions and δ 2 H-H 2 O and δ 18 O-H 2 O, respectively.The collected samples were carefully stored in a cold and dark environment until they can be transported back to the laboratory for analysis.

Analytical Methods
In situ measurements of water temperature (T), electrical conductivity (EC), and pH were conducted using portable pH (JENCO-6010N, USA) and EC (JENCO-EC3175, USA) meters.In addition, the HCO (K + , Na + , Mg 2+ , and Ca 2+ ) and trace elements (As 3+ , B 3+ , Li + , Sr 3+ , Al 3+ , Mn 2+ , Cr 3+ , Fe 2+ , Co 2+ , Cu 2+ , Zn 2+ , Ba 2+ , and Ni 2+ ) were measured by an inductively coupled plasma optical emission spectrometer (ICP-OES, IRIS Intrepid II XSP, USA) with analytical precisions of ±5%.All the analyses were conducted at the Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing.δ 2 H-H 2 O and δ 18 O-H 2 O were analyzed using an IRMS at the Institute of Resources and Environment, Henan Polytechnic University, and the isotope data were reported in per mil (‰) relative to the ratios of the Vienna Standard Mean Ocean Water (VSMOW).The analytical precisions were ±0.5‰ for δ 2 H and ±0.1‰ for δ 18 O.The δ 15 N-NO 3 and δ 18 O-NO 3 analyses were conducted with the bacterial denitrification method [59,60].This method examines the isotopic analysis of nitrous oxide (N 2 O) reduced from NO 3 − through the activity of denitrifying bacteria that lack N 2 O reductase activity, which is analyzed using an IRMS at the Environmental Stable Isotope Lab of the Chinese Academy of Agricultural Sciences.The isotope data were reported in per mil (‰) relative to atmospheric N 2 (AIR) and VSMOW.The analytical uncertainties were 0.3‰ for the δ 15 N-NO 3 − and 0.1‰ for the δ 18 O-NO 3 − .

Spatial Distribution of NO 3 − in the Shallow Groundwaters
Significant variability in NO 3 − concentrations across the studied area was observed (Figure 2a).The NO 3 − concentrations mainly ranged from 0.42 mg/L to approximately 350 mg/L, except in well SH26 (9 m depth, with a value of 651.8 mg/L).The presence of basalt at the bottom of this well acts as a NO 3 − trapping mechanism, forming a concentrated NO 3 − pool.Overall, 23.6% of the groundwater samples exceeded the permissible limit of 50 mg/L established by WHO [23].The high NO 3 − levels were governed by unconfined conditions and the thickness of the aquifer, resulting in higher concentrations in the Abu Zaabal area (i.e., vicinity of Khanka city) at the central of the study area, extending toward the northwest and east regions following the groundwater flow path (Figure 2a).The study area was characterized into three regions based on the NO 3 − concentrations: the west, middle, and east regions.The west region exhibited low NO 3 − concentrations, which can be attributed to the dilution process from recharging by the Nile River (Damietta branch) or the presence of high thickness of the upper Holocene unit that regulates the infiltration of NO 3 − into the shallow groundwater.The middle region was generally characterized by unconfined conditions (Figure 1c), along with a small thickness of the aquifer, making it highly vulnerable to the infiltration of surface pollutants.Moreover, due to the point pollution sources (e.g., cesspools and drains), NO 3 − exhibited a wide concentration range [57,61].Finally, the east region showed little impact from surface contaminants due to the increasing thickness of the upper Holocene layer.

Spatial Distribution of Hydrogeochemical Parameters
The hydrogeochemical parameters in the shallow groundwater aquifer exhibited a distinct spatial distribution pattern (Figures 2 and S5).The pH values ranged from 6.2 to 7.85, with a mean value of 7.08, indicating the groundwater's slightly acidic to neutral nature.The EC varied from 700 µS/cm to 3650 µS/cm, with an average of 1476 µS/cm (Table 1).The total dissolved solids (TDS), a critical indicator of dissolved chemical concentrations, exhibited a range of 455 mg/L and 2373 mg/L, with a mean value of 960 mg/L.The waters displayed elevated salinity levels, primarily attributed to the seepage of surface pollutants, particularly in the middle region.Furthermore, the increased extraction from well SH35 in the southeast part contributed to more significant mixing with the deep saline aquifer (Miocene aquifer) (Figure 2b).These observations aligned with previous studies by [55,57,62].The SO 4 2− and Cl − concentrations ranged from 2.5 mg/L to 827.2 mg/L (mean: 200.7 mg/L) and from 33.3 mg/L to 604 mg/L (mean: 170.3 mg/L), respectively.Compared with the previously reported values [61], the current study showed higher

Spatial Distribution of Hydrogeochemical Parameters
The hydrogeochemical parameters in the shallow groundwater aquifer exhibited a distinct spatial distribution pattern (Figures 2 and S5).The pH values ranged from 6.2 to 7.85, with a mean value of 7.08, indicating the groundwater's slightly acidic to neutral nature.The EC varied from 700 µS/cm to 3650 µS/cm, with an average of 1476 µS/cm (Table 1).The total dissolved solids (TDS), a critical indicator of dissolved chemical concentrations, exhibited a range of 455 mg/L and 2373 mg/L, with a mean value of 960 mg/L.The waters displayed elevated salinity levels, primarily attributed to the seepage of surface pollutants, particularly in the middle region.Furthermore, the increased extraction from well SH35 in the southeast part contributed to more significant mixing with the deep saline aquifer (Miocene aquifer) (Figure 2b).These observations aligned with previous studies by [55,57,62].The SO4 2− and Cl − concentrations ranged from 2.5 mg/L to 827.2 mg/L (mean: 200.7 mg/L) and from 33.3 mg/L to 604 mg/L (mean: 170.3 mg/L), respectively.Compared with the previously reported values [61], the current study showed higher SO4 2− and Cl − concentrations, which can be attributed to the enhanced seepage of surface pollutants, particularly notable in the middle region (Figure 2c,d).− concentrations (R 2 = 0.2; p = 0.3 and R 2 = 0.33; p < 0.01, respectively).As SO 4 2− and Cl − are typically enriched in wastewater, the correlations strengthened the scenario of increased recharge from the surface contaminant source.However, the insignificant Cl − and NO 3 − correlation can be attributed to biochemical mediated NO 3 − concentration attenuation.In contrast, well SH35 in the southeast part records high SO 4 2− and Cl − values, which can be mainly due to the mixing with the saline water from the underlain Miocene aquifer.In the west and east regions, the levels of these anions were not high, likely due to the thick upper Holocene layer in these regions and the dilution process in the west (Figure 2c,d).The HCO 3 − concentration showed high values in the west and southwest areas and decreased from the Damietta branch toward the east, with values ranging from 165.2 mg/L to 753.4 mg/L (mean: 390.9 mg/L).

Groundwater Recharge
The stable isotopes of water (δ 2 H/δ 18 O-H 2 O) provide valuable insights into the origin and movement of groundwater, rendering them indispensable tracers in hydrological investigations.The Global Meteoric Water Line (GMWL) is a crucial tool to interpret the isotopic tracers as it is a reference for understanding fractionation and mixing processes in natural water circulation [63,64].The Nile River, irrigation canals, and drains were the potentially important shallow groundwater sources.However, before they seeped into the groundwater, the water can undergo isotopic fractionation associated with evapotranspiration during the infiltration from the ground surface, leading to enriched values.The Quaternary aquifer can be isotopically depleted because of the hydraulic connection with the depleted underlain Tertiary aquifer.
The stable isotope composition of water samples gathered from the study area is depicted on the conventional δ 18 O-H 2 O and δ 2 H-H 2 O diagram (Figure 3).The groundwater values for δ 18 O-H 2 O and δ 2 H-H 2 O exhibit considerable diversity, spanning from −1.86‰ to 3.32‰ and from −4.46‰ to 26.61‰, respectively (Table 1).The water samples deviate below the GMWL (Figure 3), suggesting that they had been influenced by evaporation, in contrast with the old Nile water sample before Aswan High Dam (AHD) compiled by [65], which was distributed close to the GMWL.Most of the samples were distributed near the Nile water, the irrigation return flow, and wastewater endmembers (Figure 3), suggesting that these sources primarily recharged the shallow groundwater.
Water 2024, 16, x FOR PEER REVIEW 9 of 22 from −1.86‰ to 3.32‰ and from −4.46‰ to 26.61‰, respectively (Table 1).The water samples deviate below the GMWL (Figure 3), suggesting that they had been influenced by evaporation, in contrast with the old Nile water sample before Aswan High Dam (AHD) compiled by [65], which was distributed close to the GMWL.Most of the samples were distributed near the Nile water, the irrigation return flow, and wastewater endmembers (Figure 3), suggesting that these sources primarily recharged the shallow groundwater.In particular, the groundwater in the middle and western regions of the study area has undergone modern recharge, as indicated by its isotopic composition closely resembling that of the Nile water.In the west region, the isotopic values of groundwater experienced noticeable enrichment, likely due to an increase in evaporation (Figure 4).Several factors can contribute to this phenomenon.Firstly, the availability of Nile water and the prevalent traditional irrigation method, such as flood irrigation, enhance evaporation due to prolonged time on the surface before seeping downward.Secondly, In particular, the groundwater in the middle and western regions of the study area has undergone modern recharge, as indicated by its isotopic composition closely resembling Water 2024, 16, 22 10 of 22 that of the Nile water.In the west region, the isotopic values of groundwater experienced noticeable enrichment, likely due to an increase in evaporation (Figure 4).Several factors can contribute to this phenomenon.Firstly, the availability of Nile water and the prevalent traditional irrigation method, such as flood irrigation, enhance evaporation due to prolonged time on the surface before seeping downward.Secondly, the shallow depth of the water table contributed to the enrichment of the isotopic signature.Lastly, the presence of a thick upper Holocene unit exacerbated the evaporation process.Conversely, in the middle region, where this layer was absent, and there was a shortage of Nile water coupled with increased groundwater abstraction to compensate for this shortage, the isotopic composition of the groundwater remained closer to that of the Nile water and drainage systems.In the east region, where the upper Holocene layer is thick and there is shortage of the Nile water, the abstraction of the groundwater increased, which resulted in well nos.SH43, SH17, SH35, SH50, SH46, and SH38.2 being affected by mixing with the Tertiary aquifer.These findings are consistent with previous studies conducted by [51,66].These results show that, although the NO 3 − groundwater pollution in the west/east regions was low, it can result from irrigation water enriched with CF and SON.This low concentration was due to the dilution of excess irrigation water and the Nile water recharging in the west.
Water 2024, 16, x FOR PEER REVIEW 10 of 22 which resulted in well nos.SH43, SH17, SH35, SH50, SH46, and SH38.2 being affected by mixing with the Tertiary aquifer.These findings are consistent with previous studies conducted by [51,66].These results show that, although the NO3 − groundwater pollution in the west/east regions was low, it can result from irrigation water enriched with CF and SON.This low concentration was due to the dilution of excess irrigation water and the Nile water recharging in the west.In contrast, in the east, the dilution that resulted from the mixing with the deep groundwater contributed to the low NO3 − concentrations.However, the relatively high NO3 − (28.8 mg/L in well SH35) southeast of the study area could have originated from the lateral groundwater flow with high NO3 − concentration due to relatively intense abstraction (250 m3/day).In contrast, in the middle region, more wastewater is loaded into the groundwater due to unconfined conditions.In contrast, in the east, the dilution that resulted from the mixing with the deep groundwater contributed to the low NO 3 − concentrations.However, the relatively high NO 3 − (28.8 mg/L in well SH35) southeast of the study area could have originated from the lateral groundwater flow with high NO 3 − concentration due to relatively intense abstraction (250 m3/day).In contrast, in the middle region, more wastewater is loaded into the groundwater due to unconfined conditions.

−
Cl − serves as a reliable indicator of wastewater and fertilizer impacts, which can contribute to elevated Cl − levels and is unaffected by chemical, physical, and biological processes [45,46,67].The correlation between Cl − and NO 3 − /Cl − is widely utilized for source identification of NO 3 − sources in water, specifically for distinguishing agricultural or/and wastewater sources [45,47] and for distinguishing between the influences of dilution and denitrification on NO 3 − levels [68].A high NO 3 − /Cl − ratio coupled with low Cl − levels indicates that agricultural sources (e.g., chemical fertilizer) and soil organic nitrogen (SON) are the main contributors of NO 3 − in the groundwater.Conversely, a low NO 3 − /Cl − ratio and high Cl − content suggest wastewater sources as the primary origin of NO 3 − contamination [27,69].
Most of the groundwater samples had NO 3 − /Cl − ratios < 1 and relatively high Cl − concentrations (Figure 5a), suggesting a probable dominance of wastewater as the NO 3 − source [68,70].However, a few samples in the middle region (SH26 and SH36; Figure 5a) exhibited high NO 3 − /Cl − ratios > 1, which can be linked to a combination of SON and CF with wastewater inputs [70] (Figure 5a).The significant correlation between SO 4 2− and NO 3 − of the groundwaters in the middle region supported the dominant role of wastewater (Figures 5b and 6b) [71][72][73].A few points were scattered from the correlation, which can be ascribed to the evaporate (e.g., gypsum) dissolution in the arid region [74,75] or as a result of using CF enriched with SO 4 2− [13,76].In addition, most of the groundwater samples in the study area exhibited TDS concentrations below 1000 mg/L associated with a low (NO 3 − + Cl − )/HCO 3 − ratio.The correlation is strongly positive (R 2 = 0.71; p < 0.01) in the middle region, which can be attributed to the substantial reduction condition and then denitrification, which attenuates the NO 3 − and/or produce more HCO 3 − [70,77] (Figure 5c).This speculation can then be consistent with the theoretical denitrification defined in Equation (1) [78,79].In the west and east regions, this relationship is a weak positive correlation as a result of the impacts of SON and CF [73,80] associated with biodegradation of organic matter, which is rich in the upper Holocene layer in these regions and consequently increase HCO 3 − concentration [81].
The dual NO 3 − isotope approach (δ 15 N-NO 3 and δ 18 O-NO 3 ) is widely recognized as a powerful technique for constraining NO 3 − sources and behaviors [9,38,45,50,82].Different NO 3 − sources exhibit characteristic isotopic signatures of δ 15 N-NO 3 and δ 18 O-NO 3 , which can be used to trace their origins [38,83,84].Figure 7a shows the δ 15 N-NO 3 and δ 18 O-NO 3 values of the groundwaters, Nile water, and potential endmembers in the study area.The isotopic compositions of δ 15 N-NO 3 and δ 18 O-NO 3 in the groundwaters showed wide ranges, ranging from −23.4‰ to 75.4‰ (mean: 8.92‰) and from −14.3‰ to 39.8‰ (mean: 10.53‰), respectively (Table 1).The groundwaters in the middle region have δ 15 N-NO 3 and δ 18 O-NO 3 ranging from 4‰ to 24.4‰ and from 10‰ to 23.9‰, respectively (Figures 4 and 7).As expected, the data are distributed near the endmembers for SON and CF and wastewater, suggesting that these anthropogenic sources should be the major sources of the groundwaters (Figure 7a).Due to their analogous isotopic compositions and transport routes, we merged SON and CF as one source.The direct input of atmospheric precipitation should be minor because the study area experiences minimal precipitation (Figure 7a).and 7a).The observation gives us the confidence that the prevalent denitrification proces counterbalanced the excess NO3 − loading to the groundwater to some extent (Figure 7a The presence of clay lenses and clayey sediments in the aquifer can enhance th denitrification [38,85] by providing soluble organic carbon and anaerobic conditions [77 However, more excess NO3 − loading into the groundwater can inhibit this process an result in high NO3 − levels (e.g., SH26 and SH32).By contrast, no relationships existed between the dual isotopes in the samples collected in the west/east regions (Figure 6a and Figure 7b), indicating minor denitrification.The groundwater samples in the west and east regions exhibited relatively depleted and constrained δ 15 N-NO3 values (Figure 4 and Figure 7a).Their δ 15 N-NO3 and δ 18 O-NO3 compositions ranged from −23.3‰ to 4‰ and from −13.6‰ to 10‰ respectively.Most of these samples had δ 15 N-NO3 values lower than most 15 N-depleted SON and CF endmember, which can be ascribed to nitrification processes.Nitrification would inhibit nitrification.The speculation is supported by the low NO3 − concentrations (Figure 4 and Figure 7a).Collectively, the low isotopic values and concentrations of NO3 − in the west/east regions should be attributed to the nitrification process, which also can be enhanced in the west due to the long residence time of water on the surface before it seeps into the groundwater [86].Notably, although sample SH35 is collected from a deep well (depth = 156 m), it showed a NO3 − value of 28.8 mg/L; this observation can result from NO3 − recharging to the deep zone through the lateral groundwater flow.Notably, a number of the isotopic values, especially those in the middle region, are higher than all the endmembers, and there is a significant positive correlation between the dual isotopes with a slope of 0.48 (R 2 = 0.39, p < 0.0001) (Figures 4, 6b and 7), which is the typical isotopic signal for biological NO 3 − removal [38].Denitrification in groundwaters is well documented, leading to an exponential co-increase in δ 15 N-NO 3 and δ 18 O-NO 3 , with values exceeding 100‰ recorded [38].The significant denitrification is also supported by the simultaneous decreasing NO 3 − levels and increasing dual isotopic values (Figures 6b and 7a).The observation gives us the confidence that the prevalent denitrification process counterbalanced the excess NO 3 − loading to the groundwater to some extent (Figure 7a).The presence of clay lenses and clayey sediments in the aquifer can enhance the denitrification [38,85] by providing soluble organic carbon and anaerobic conditions [77].However, more excess NO 3 − loading into the groundwater can inhibit this process and result in high NO 3 − levels (e.g., SH26 and SH32).By contrast, no relationships existed between the dual isotopes in the samples collected in the west/east regions (Figures 6a and 7b), indicating minor denitrification.The groundwater samples in the west and east regions exhibited relatively depleted and constrained δ 15 N-NO 3 values (Figures 4 and 7a).Their δ 15 N-NO 3 and δ 18 O-NO 3 compositions ranged from −23.3‰ to 4‰ and from −13.6‰ to 10‰, respectively.Most of these samples had δ 15 N-NO 3 values lower than most 15 N-depleted SON and CF endmember, which can be ascribed to nitrification processes.Nitrification has a substantial fractionation effect, with 14 N being preferentially nitrified in NH 4 + plentiful environments.The anthropogenic activities should discharge a large amount of NH 4 + containing wastewater and irrigation discharge to the groundwaters, resulting in NH 4 + plentiful conditions.Yet, the overall anaerobic environments in the groundwaters would inhibit nitrification.The speculation is supported by the low NO 3 − concentrations (Figures 4 and 7a).Collectively, the low isotopic values and concentrations of NO 3 − in the west/east regions should be attributed to the nitrification process, which also can be enhanced in the west due to the long residence time of water on the surface before it seeps into the groundwater [86].Notably, although sample SH35 is collected from a deep well (depth = 156 m), it showed a NO 3 − value of 28.8 mg/L; this observation can result from NO 3 − recharging to the deep zone through the lateral groundwater flow.
Overall, according to the water chemistry and isotopic tracers, we found that wastewater and SON and CF were the major sources of shallow groundwaters.Denitrification is the primary process that occurs in the middle region accompanied by excess NO 3 − loadings, whereas the west/east regions can be affected by zonal nitrification.

Identification of NO 3 − Transformation Process Coupled with Mn Oxides Reduction
The presence of trace elements in groundwater provides valuable insights into NO 3 − dynamics [12,87].Among these trace elements, Mn 2+ , Fe 2+ , and Cu 2+ play crucial roles in denitrification by enhancing the rate of this process [44].Notably, the relationship between oxidation and reduction of Mn and Fe in natural waters extends beyond the typical redox conditions necessary for their mobilization [88].Mn and Fe in minerals serve as electron acceptors for denitrifying bacteria [77], thereby facilitating denitrification and ultimately enhancing denitrification rates [43,44,89].The concentrations of Mn 2+ in the groundwaters ranged from 0.002 mg/L to 3.38 mg/L, with a mean value of 0.83 mg/L.Furthermore, it is noteworthy that 65.5% of the groundwater samples examined exceeded the permissible limit of 0.4 mg/L set by the WHO (Figure S6).There were significant correlations between the Mn 2+ concentrations and the δ 15 N-NO 3 and δ 18 O-NO 3 values in the middle region (p < 0.01; Figures 6b and 8a,b), implying the role of Mn in regulating the prevalent denitrification.The speculation was also supported by the negative correlation between Mn 2+ and NO 3 − concentrations (Figures 6b and 8c).In addition, in the west/east region, the above correlations were absent (Figures 6a and 8a,c), further giving us the confidence that the biogeochemistry of Mn and denitrification were tightly coupled.This observed relationship was in line with the results of an experimental study that showed that MnO 2 addition enhanced the denitrifying bacteria's metabolism and removed about 99% of the NO 3 − and released Mn 2+ in weak acidic and neutral conditions [43].However, reducing the Fe/Mn oxides coupled with nitrification-denitrification under anaerobic conditions and replacing the need for O2 can be prevalent in these areas, where NH4 + oxidized and turned to NO3 − or N2 (i.e., anammox) based on Equation (2) [78].
NH4 + + 1.31 NO2 − + 0.066 HCO3 − + 0.13 H + → 1.02 N2 + 0.26 NO3 − + 0.066 CH2O0.5N0.15 + 2.03 H2O (2) These findings highlight the importance of considering the biogeochemistry of trace elements, particularly Mn 2+ , in assessing and managing NO3 − contamination in shallow groundwater.However, it is important to note that while denitrification mitigates NO3 − excess, it cannot fully offset the increasing NO3 − loading into the groundwater.Due to this The potential source of Mn in the study area is the upper Holocene layer [90], which is also enriched in organic matter and Mn minerals, leading to reduced environments [91].Mn is commonly present in insoluble Mn(IV) and Mn(III), and their reduction will generate soluble Mn 2+ [88,90].In addition, Mn can result from CF utilized in the fruit farms in the western region [92].We observed co-increasing of Mn 2+ with HCO 3 − , Fe 2+ , and Ba 2+ (Figures 6 and 8e-g).As HCO 3 − , Fe 2+ , and Ba 2+ concentrations are closely related to chemical weathering, high Mn 2+ in the groundwaters should be associated with chemical weathering processes.The mafic rocks are enriched with Mn [88] and the origin of the Nile silts and the Quaternary deposits as a result of weathering of these rocks [93], which lead to sediment enriched with Mn oxides.In contrast, there was no significant relationship between Mn 2+ and SO 4 2− in the middle region (Figures 6b and 8h), indicating that the anthropogenic contribution of Mn 2+ was less significant.However, Mn 2+ and SO 4 2− showed a significant positive correlation in the west/east regions (Figures 6a and 8h), indicating the direct input of Mn 2+ from anthropogenic sources [81,91].That is, Mn was largely in an oxidized form in this layer before entering the water body, and it cannot participate in the reduction of NO 3 − .As the predominant factors influencing the concentrations of Mn 2+ in the shallow groundwaters in the west/east and middle regions of the study area are quite different, the increase in Mn 2+ concentrations and the associated redox process in the middle region enhanced denitrification, while in the west/east regions, denitrification and Mn 2+ concentrations were decoupled.
However, reducing the Fe/Mn oxides coupled with nitrification-denitrification under anaerobic conditions and replacing the need for O 2 can be prevalent in these areas, where NH 4 + oxidized and turned to NO These findings highlight the importance of considering the biogeochemistry of trace elements, particularly Mn 2+ , in assessing and managing NO 3 − contamination in shallow groundwater.However, it is important to note that while denitrification mitigates NO 3 − excess, it cannot fully offset the increasing NO 3 − loading into the groundwater.Due to this process, there is a higher release of Mn 2+ , which, when combined with an excess of NO 3 − , poses a potential health risk to the residents.

Conclusions
In the present investigation, the hydrogeochemical parameters and multi-isotope tracers were used to identify the sources and transformation of NO 3 − in the shallow groundwater in the southeast of the Nile Delta region for the first time.Our findings reveal that the NO 3 − values ranged from 0.42 mg/L to 650 mg/L and the groundwater in the middle region was highly impacted by NO 3 − pollution.The NO 3 − pollution in the west/east regions was relatively weak due to a thick upper Holocene layer or as a result of the dilution process by the Nile River recharge in the west or the mixing with deep groundwater in the east.According to the WHO guidelines for drinking water, the criterion for NO 3 − and Mn 2+ is exceeded in 23.6% and 65.5% of shallow groundwater samples, respectively.The values of δ18O-NO 3 and δ15N-NO 3 between −14.32‰ and −39.79‰ and between −23.4‰ and -75.42‰, respectively, implied that wastewater and SON and CF were the main NO 3 − sources.NO 3 − in the west/east regions can be derived from SON and CF associated with zonal nitrification.While in the middle region, NO 3 − was more derived from the wastewater, and the denitrification was prevalent.Remarkably, the denitrification might be closely coupled with the biogeochemical cycling of Mn.Finally, the data obtained from this study bear significant implications across several dimensions.Firstly, it establishes the first reference for NO 3 − isotope investigations of the groundwater in Egypt.Secondly, it is poised to furnish valuable insights to coupling Mn +2 and NO 3 − biogeochemical dynamics in the arid region, delineating pivotal denitrification and Mn reduction relationships.

Figure 1 .
Figure 1.Maps of the study area and the sampling sites.(a) Landsat 8 and depth to the water table;(b) digital elevation model (DEM) and aquifer thickness; and (c) thickness of the upper semiconfined aquifer layer (modified from[53]) and hydraulic head.

Figure 1 .
Figure 1.Maps of the study area and the sampling sites.(a) Landsat 8 and depth to the water table;(b) digital elevation model (DEM) and aquifer thickness; and (c) thickness of the upper semi-confined aquifer layer (modified from[53]) and hydraulic head.

Figure 2 .
Figure 2. Spatial distribution maps of hydrogeochemical parameters of the groundwater in the study area: (a) TDS; (b) NO 3 − ; (c) SO 4 2− ; and (d) Cl − .The high SO 4 2− and Cl − concentrations in the middle region of the study area were consistent with the high NO 3 − concentrations (R 2 = 0.2; p = 0.3 and R 2 = 0.33; p < 0.01, respectively).As SO 4 2− and Cl − are typically enriched in wastewater, the correlations strengthened the scenario of increased recharge from the surface contaminant source.However, the insignificant Cl − and NO 3 − correlation can be attributed to biochemical mediated NO 3 − concentration attenuation.In contrast, well SH35 in the southeast part records high SO 42− and Cl − values, which can be mainly due to the mixing with the saline water from the underlain Miocene aquifer.In the west and east regions, the levels of these anions were not high, likely due to the thick upper Holocene layer in these regions and the dilution process in the west (Figure2c,d).The HCO 3 − concentration showed high values in the west and southwest areas and decreased from the Damietta branch toward the east, with values ranging from 165.2 mg/L to 753.4 mg/L (mean: 390.9 mg/L).

Figure 4 .
Figure 4. Spatial distribution maps of the δ 2 H-H 2 O, δ 18 O-H 2 O, δ 15 N-NO 3 , and δ 18 O-NO 3 of the groundwater in the study area.

Figure 6 .
Figure 6.Plot of the Pearson correlation matrix of hydrogeochemical and isotope data of the shallow groundwater in the (a) west/east regions and (b) middle region.* p < 0.05; ** p < 0.01; *** p < 0.001.

Figure 7 .
Figure 7. (a) Relationship between δ 15 N-NO3 and δ 18 O-NO3 values of the groundwater and endmember samples, with the ranges of potential nitrate sources.(b) δ 15 N-NO3 versus δ 18 O-NO3 of the groundwater samples in the study area.

Figure 7 .
Figure 7. (a) Relationship between δ 15 N-NO 3 and δ 18 O-NO 3 values of the groundwater and endmember samples, with the ranges of potential nitrate sources.(b) δ 15 N-NO 3 versus δ 18 O-NO 3 of the groundwater samples in the study area.

Table 1 .
Descriptive statistics of analyzed parameters of shallow groundwater and endmember samples in the study area.