Long-Term Changes in Fish Landings and Fish Community Structure in Nile Delta Lakes: Implications for Fisheries Sustainability

Abstract

This study examined long-term trends (1991–2019) in landings and fish community structure in the four Egyptian Nile Delta lakes. Using fisheries data, we explored trends in the catch per unit effort (CPUE) and temporal dynamics of landings and fishing effort. Non-metric Multidimensional Scaling (nMDS) and Similarity Percentage Analysis (SIMPER) were employed to assess long-term changes in fish community structure. The results revealed variable productivity across the lakes. Lake Manzala often exhibited higher yields between 1991 and 2004, and notably in 2013 (e.g., 62,372 tons), while Lake Burullus peaked at 81,399 tons in 2019. A reciprocal trend was often observed in their total yields. Lake Burullus catches were dominated by Tilapia and Mullets, while Edku and Mariout showed lower productivity. CPUE patterns varied, with Lake Manzala showing a notable increase, peaking at approximately 52 tons per boat per year in 2013, and Lake Burullus experienced a sharp increase to about 29 tons per boat per year in 2019. A shift towards amateur fishing was observed predominantly in Lake Manzala, alongside a decline in traditional licensing. An increase in fishers operating without boats was also noted across all the Northern Lakes, with contributions from Lake Edko and Lake Manzala. nMDS and SIMPER analyses revealed distinct temporal groupings of years within each lake, indicating significant shifts in fish community structure, likely in response to invasive species, pollution, and habitat degradation. These findings underscore the need for lake-specific management and long-term monitoring to address unsustainable fishing and ecological changes, ensuring biodiversity conservation and fisheries sustainability in the region.

1. Introduction

Aquatic ecosystems worldwide are experiencing dramatic alterations due to escalating anthropogenic activities, resulting in significant biodiversity loss. Overfishing, coastal degradation, habitat destruction, invasive species introductions, damming, climate change, and increased organic pollution have collectively created severe challenges for aquatic biodiversity [1,2,3,4]. Coastal ecosystems, in particular, are among the most severely impacted, facing considerable disruptions to their ecological integrity [5], with specific examples including coral reefs, mangrove forests, salt marshes, seagrass beds, and estuaries. This instability threatens not only the diverse life within these systems, but also the essential ecosystem services they provide, such as water and fishery resources. Consequently, the systematic monitoring and conservation of these ecosystems have become critical global priorities to prevent further losses [6,7].

The urgency of conservation is underscored by the United Nations’ 2030 Sustainable Development Goals (SDGs), particularly Goal 14, which emphasizes ocean health and aquatic biodiversity. This goal highlights the need for enhanced scientific understanding and sustainable marine resource management, especially in low- and middle-income countries where ecosystems are often more vulnerable and less resilient to change. Biodiversity studies are crucial for establishing baseline data to track human-induced and climate-driven shifts, yet research on fish diversity and functionality in human-impacted estuarine ecosystems has historically been limited [8].

Lakes are equally vulnerable to multifaceted threats, including species dispersal dynamics, invasive species expansion, eutrophication, acidification, intensified land use, water abstraction, hydrological modifications, and climate change [9]. Among these, the Nile Delta lakes, vital ecosystems supporting significant biodiversity and local livelihoods, are also facing increasing environmental pressures, such as pollution and overfishing. The resilience and recovery of lakes in response to these changes are pivotal research areas for effective biodiversity conservation [10]. Fish, the most diverse vertebrate group in freshwater ecosystems, serve as ecological health indicators, but are also highly threatened by human activities such as river management, dam construction, pollution, land use changes, and overfishing [3]. Despite known threats, comprehensive impacts on fish biodiversity remain under-explored, necessitating urgent and robust biodiversity surveys [11,12]. Therefore, the lack of long-term data within the Nile Delta compounds the global issue of poor monitoring.

Fish diversity is particularly informative as a bioindicator due to its reflection of a wide range of environmental conditions [13]. The complex interaction of climate change and human activities complicates the spatial and temporal dynamics of fish assemblages, an area requiring further documentation [14]. Seasonal and annual variations in fish community structure are influenced by species’ tolerance to local environmental conditions and invasive species effects [15]. Environmental changes can also alter species’ dispersal capacities, affecting their distribution and abundance [16]. Metal pollution, eutrophication, and overfishing pose significant risks to biodiversity, leading to declines in species diversity and average body size [5,17,18,19].

Furthermore, advancements in fishing technologies, fleet overcapacity, and illegal fishing have contributed to global fish population declines. The Food and Agriculture Organization (FAO) reported that approximately 33% of fish stocks were at biologically unsustainable levels in 2015, up from 10% in 1974 [20]. This trend underscores the need for comprehensive long-term data to address species loss and identify ecological drivers.

Reliable indicators and data are essential for understanding fish community responses to anthropogenic impacts and for restoring ecosystem services. There is a growing demand for cost-effective biodiversity assessment methods. Historical data analysis and local ecological knowledge can provide valuable insights into environmental changes. Fisheries landings data offer insights into fishery trends, sustainability, and ecosystem health through analyses of total landings, average fish size, catch per unit effort (CPUE), and trophic levels.

Fisheries in Egypt are economically significant, supporting millions of livelihoods. While aquaculture dominates fish production, wild fisheries from the Nile Delta lakes contribute over 36% of Egypt’s annual fish landings [21,22]. However, recent aquaculture-focused policies led to a 22.8% decline in wild fisheries’ production from 1997 to 2012 [21,22]. This decline was largely due to the conversion of natural wetlands and traditional fishing grounds into aquaculture farms, resulting in habitat loss and degradation for wild fish populations. Furthermore, increased water demand by aquaculture operations reduced water availability and quality for wild fisheries, while practices such as untreated wastewater discharge and the escape of farmed fish sometimes introduced diseases to wild stocks. Research on fisheries in the Nile Delta is limited, with existing studies primarily found in gray literature and local journals that have restricted international dissemination. While many studies on these lakes focus on pollution levels and contaminant analysis, fisheries-specific investigations are scarce. Critically, no previous studies have utilized long-term data spanning nearly three decades to assess changes in fish landings and species community structure.

This study aimed to examine the long-term trends (from 1991 to 2019) in fish community structure and landings across the Nile Delta lakes, comparing fish landings and CPUE among the lakes to understand variations in productivity and fishing efficiency; analyzing annual changes in landings composition to identify long-term shifts in fish communities; and quantifying the specific contributions of dominant fish species to the observed changes in community structure using multivariate statistical techniques. By achieving these objectives, this research seeks to provide critical insights into the ecological dynamics of these vital aquatic ecosystems and inform future conservation and management strategies.

2. Material and Methods

2.1. Study Area

Along the Egyptian Mediterranean coast, there are five brackish lakes, collectively known as the Northern Lakes (Figure 1). This study focuses on the following four of these lakes, situated within the Nile Delta: Lake Mariout, Lake Edku, Lake Burullus, and Lake Manzala (from west to east). Except for Lake Mariout, all have direct connections to the Mediterranean Sea and receive Nile water via multiple irrigation canals.

Lake Mariout, the smallest of the Nile Delta lakes, is located at 31°07′ N, 29°57′ E. This shallow lake, with depths reaching approximately 1.5 m, is a remnant of the prehistoric Mareotis Lake. East of Lake Mariout and west of the Rosetta branch of the Nile lies Lake Edku (30°08′30″ E to 30°23′00″ E, 31°10′ N to 31°18′ N). Its area has significantly decreased due to agricultural expansion, and it receives substantial wastewater discharge from three major drains on its eastern side. Lake Burullus, positioned between the Rosetta and Damietta branches of the Nile, is an elongated lake with approximately 50 small islands. Separated from the Mediterranean Sea by a sand barrier, it extends roughly 65 km in length, with widths varying from 6 to 16 km and water depths ranging from 0.4 to 2.0 m (west to east). Lake Manzala, located at the northeastern tip of the Nile Delta, is separated from the Mediterranean Sea by a narrow sandy strip, connected by two main outlets, El-Gamil 1 and 2. Bordered by the Suez Canal to the east and agricultural lands to the south, it is the largest shallow lake in the region, measuring 45 km in length and 25 km in width.

2.2. Data Collection and Analysis

Annual fish landings and fishing effort data for the four Nile Delta lakes from 1991 to 2019 were obtained from the General Authority for Fisheries Resources and Development (GAFRD, 1991–2019), the official agency responsible for managing Egypt’s fisheries resources. This agency, now known as the Lakes and Fisheries Resources Protection and Development Agency (LFRPDA), is the primary source of historical fish landings and fishing effort data, as referenced in numerous previous studies [21,23,24]. GAFRD began collecting data and publishing annual statistical books in the early 1990s. Landings data are gathered through a combination of comprehensive inventory in closed ports and a sampling method in open sites [25]. While the sampling method carries a risk of catch underestimation, these official data, consistent over the study period, are the sole long-term national source and are provided to international organizations like the FAO. Fishing effort and capacity data, collected annually by GAFRD offices from registered vessels, are considered reliable for representing official registered vessels (excluding IUU). Annual fish landings biomass (tons) was used to analyze historical variations at the annual (tons year⁻¹) scale, as well as for individual species. Data on fishing effort, including the number of operational boats (registered in the GAFRD lake branch), one-year licenses, five-year licenses, amateur fishers, and fishers without boats, were also compiled and summarized. It should be noted that the GAFRD does not provide statistics on boat length or gross tonnage in their annual statistical book for inland and lake fisheries.

To examine annual variations in fish community structure (landings or catch composition) from 1991 to 2019, non-parametric analyses were conducted using Non-metric Multidimensional Scaling (nMDS) and Similarity Percentage Analysis (SIMPER) [26,27]. For each lake, annual landings composition data were organized into a matrix, with years as rows and fish species as columns, containing the biomass of each species per year. Pairwise ecological distances between years were calculated using the Bray–Curtis dissimilarity (or similarity) index, a standard measure for assessing compositional dissimilarity based on species abundance or biomass. This resulted in a dissimilarity matrix for each lake. Subsequently, nMDS was employed to reduce the high-dimensional dissimilarity matrix into a two-dimensional space for visualization, preserving the rank order of dissimilarities rather than exact distances. The stress value, displayed in the top right corner of each plot, indicates the goodness of fit, with lower values representing a better fit. Generally, stress values below 0.10 are considered a good fit for nMDS, with values below 0.05 indicating an excellent representation. For the present analysis, the stress values obtained were 0.08 (Burullus), 0.05 (Edko), 0.07 (Manzala), and 0.03 (Mariout), all of which confirm a very good two-dimensional representation of the community structure. The similarity scale, expressed as a percentage, reflects the within-group similarity, determined by applying a threshold to the Bray–Curtis similarity values. While cluster analysis is also commonly used to delineate ecological assemblages, it was not included, as the combination of nMDS for visualizing continuous temporal shifts and SIMPER for detailing species contributions was considered to fully address the study’s aims, making further clustering redundant.

To identify the species contributing to the differences between groups identified by Non-metric Multidimensional Scaling (nMDS), Similarity Percentages (SIMPER) analysis was performed. This analysis calculated the average within-group similarity and species contributions using the Bray–Curtis similarity index [28] on annual landings biomass (tons year⁻¹). Specifically, SIMPER determined (1) the average Bray–Curtis similarity within each group based on species biomass; (2) the percentage contribution (Cont. %) of each species to the average similarity, highlighting key species responsible for group similarity; and (3) the average biomass (Av. Bio.) of each contributing species. A 5% cut-off was applied, selecting only species contributing more than 5%. All multivariate analyses, including nMDS, Bray–Curtis calculations, and SIMPER, were conducted using the PRIMER v6 (Plymouth Routines in Multivariate Ecological Research) software package.

3. Results

3.1. Annual Changes in Landings, Fishing Effort, and CPUE

The trends in fish landings from the four Nile Delta lakes between 1991 and 2019 are presented in Figure 2. The individual lake landings show that Lake Burullus consistently yielded the highest catches, peaking in recent years, while Lake Edko displayed relatively stable, lower yields and Lake Manzala exhibited more volatile but generally higher yields than Lake Edko, also showing a continuous growth trend in recent years and reaching a peak in 2019 (Figure 2A). Lake Mariout exhibited the lowest landings overall. The total natural fisheries yield for the Nile Delta lakes showed fluctuations over the study period, with maximum values observed in 1999 and between 2001 and 2003, and a continuous increase noted since 2017 (Figure 2B). The right axis highlights the percentage contribution of these lakes to Egypt’s total fisheries, fluctuating around 40% with a slight upward trend. Further analysis of the percentage contribution of each individual lake to the total Nile Delta lakes’ yield revealed that the contribution rates of Lake Manzala and Lake Burullus were often comparable, frequently showing an inverse relationship, where an increase in one’s contribution corresponded with a decrease in the other’s (Figure 2C). These data suggest a shift in the relative importance of these lakes for Egypt’s fisheries, with Lake Burullus emerging as a critical resource.

The analysis of fishing activity across four Egyptian lakes from 2001 to 2019 revealed significant variations in boat numbers and licensing trends (Figure 3). Fishing effort, expressed as the total number of boats, showed a general decline over time, with Lake Burullus consistently exhibiting the highest boat counts (Figure 3A). On the other hand, a sharp decrease in 1-year fishing licenses was observed, particularly in Lake Burullus in the earlier years, though an abnormal surge was noted in 2018. For Lake Edko, the number of 1-year fishing licenses showed the process of an initial decrease followed by an increase since 2013, accounting for a high proportion in later years, except for 2018, while Lakes Manzala and Mariout maintained relatively stable and low numbers (Figure 3B). A similar trend in 5-year licenses was also observed, with a noticeable decline in Lake Burullus (Figure 3C). However, a surge in amateur fishing licenses was observed in recent years, predominantly in Lake Manzala (Figure 3D). Similarly, an increase in the number of fishers operating without boats was observed (across all Northern Lakes), with notable contributions from Lake Edko and Lake Manzala in different periods, while the numbers for Lake Burullus and Mariout remained very low (Figure 3E). These trends suggest a shift in fishing practices and regulations, with a potential transition towards amateur fishing and an increase in informal fishing activities, particularly within Lake Burullus.

The catch per unit effort (CPUE), measured in tons per boat per year, exhibited distinct patterns across the four Egyptian lakes from 2001 to 2019 (Figure 4). Lake Manzala showed a notable increase in CPUE, particularly after 2012, peaking at around 50 tons per boat per year. In contrast, Lake Burullus displayed a relatively stable CPUE of around 10 tons per boat per year, with a slight increase in recent years. Lakes Edko and Mariout consistently showed the lowest CPUE values, generally below 10 tons per boat per year, though a sharp increase was observed in 2019, reaching nearly 30 tons per boat per year. These findings suggest a significant improvement in fishing efficiency or resource availability in Lake Manzala, while the other lakes maintained relatively stable or low levels of productivity.

3.2. Annual Changes in Fish Community Structure

The composition of fish landings across the four Egyptian lakes (Burullus, Edko, Manzala, and Mariout) revealed distinct patterns in both total volume and species diversity for the study period (Figure 5). The total landings (tons) for each lake highlighted variations in yield and species contributions (Figure 5A,C,E,G). While a frequent reciprocal trend was observed in their total yields, Lake Burullus and Lake Manzala displayed comparable high landings over the study period (as shown previously in Figure 2A). Lake Burullus landings were dominated by Tilapia (Oreochromis niloticus and Oreochromis aureus) and Mullets (Mugilidae), with a notable presence of European Seabass (Dicentrarchus labrax) and A. Catfish (Clarias gariepinus) (Figure 5A). Lake Edko landings were primarily composed of Tilapia (O. niloticus and O. aureus) and A. Catfish (C. gariepinus), with a decreasing trend over time (Figure 5C). Manzala’s landings featured diverse catches, including Tilapia (O. niloticus and O. aureus), S. Smelts (Atherina hepsetus), A. Catfish (C. gariepinus), and Mullets (Mugilidae), with Crabs (Portunus spp.) also contributing in high quantities, particularly during the early years from 1991 to approximately 1998 (Figure 5E). Mariout, despite showing lower overall landings, displayed a significant increase in later years, with Tilapia (O. niloticus and O. aureus) and A. Catfish (C. gariepinus) being the dominant species (Figure 5G).

The percentage composition of these landings provides insights into the relative importance of different species within each lake’s fishery (Figure 5B,D,F,H). In Burullus, Tilapia consistently constituted a significant portion of the catch, though its dominance fluctuated (Figure 5B). Edko’s landings were characterized by a high percentage of Tilapia, with other species contributing minimally (Figure 5D). Manzala showed a more diverse composition, with Tilapia maintaining a substantial proportion and A. Catfish generally showing a higher proportion than S. Smelts, particularly after 2000, during which S. Smelts remained at a relatively low level (Figure 5F). Mariout’s species composition shifted over time, with A. Catfish becoming increasingly prominent, alongside Tilapia (Figure 5H). These findings underscore the dynamic nature of fish populations and the varying ecological and economic roles of different species in each lake’s fishery.

The Non-metric Multidimensional Scaling (nMDS) ordinations, based on Bray–Curtis similarity, revealed temporal shifts in fish community structure across the four Egyptian lakes for the study period. Figure 6 shows distinct groupings of years, indicating periods of similar species composition. Lake Burullus exhibited four distinct groups (A–D), suggesting significant community changes over time, with recent years forming a separate cluster (Figure 6A). Lake Edko showed less temporal variation, primarily clustering into two main groups (A and C) with some outliers (Figure 6B). Lake Manzala displayed four groups, indicating moderate community shifts, with a notable separation of recent years (Figure 6C). Lake Mariout also revealed four groups, highlighting substantial temporal changes, particularly in the later period (Figure 6D). These results suggest that while all lakes experienced community turnover, the magnitude and timing of these changes varied, potentially reflecting differences in environmental pressures or management practices.

The SIMPER analysis, complementing the nMDS ordination results, revealed the specific species contributing to the observed temporal groupings in fish community structure across the four Egyptian lakes (

Table 1. SIMPER analysis results detailing the average similarity, species contributions, average biomass, and percentage contribution of species within each group identified by Non-metric Multidimensional Scaling (nMDS) for the four Egyptian lakes (Burullus, Edko, Manzala, and Mariout). Similarity among samples was calculated using the Bray–Curtis similarity index on annual landings biomass (tons year⁻¹). Species contributing over 5% to the average within-group similarity are shown, highlighting the key species driving the observed patterns in fish community structure.

Burullus	Group A			Group B			Group C			Group D
	Av. Similarity: 93.40			Av. Similarity: 88.08			Av. Similarity: 89.69			Av. Similarity: 87.49
	Species	Av. Bio.	Cont.%	Species	Av. Bio.	Cont. %	Species	Av. Bio.	Cont. %	Species	Av. Bio.	Cont. %
	Tilapia	23,514,5	48.68	Tilapia	35,215,93	67.8	Tilapia	20,400,33	40.1	Tilapia	38,445,13	60.16
	Mullets	10,404	21.68	Mullets	9853,47	16.76	Mullets	11,855	18.36	Mullets	10,969,88	18.1
	Others	5388,5	11.03	Others	3900	5.58	A. catfish	10,008,33	18.28
	A. catfish	3734	6.74
	S. Seabass	2914	6.1
Edko	Group A			Group B			Group C
	Av. Similarity: 92.22			Av. Similarity: 92.18			Av. Similarity: 91.64
	Species	Av. Bio.	Cont.%	Species	Av. Bio.	Cont. %	Species	Av. Bio.	Cont. %
	Tilapia	7586,38	81.09	Tilapia	8166,17	87.54	Tilapia	8166,17	87.54
	Others	897,75	9.69	G. carp	817,33	7.84	G. carp	817,33	7.84
Manzala	Group A			Group B			Group C			Group D
	Av. Similarity: 85.14			Av. Similarity: 90.93			Av. Similarity: 84.70			Av. Similarity: 83.99
	Species	Av. Bio.	Cont.%	Species	Av. Bio.	Cont. %	Species	Av. Bio.	Cont. %	Species	Av. Bio.	Cont. %
	Tilapia	36,309,38	65.55	Tilapia	34,681	51.49	Tilapia	27,500,67	46.62	Tilapia	19,965	50.71
	Others	12,559,5	17.05	A. catfish	10,429	15.65	Mullets	16,249,75	25.61	A. catfish	7329,2	17.4
	A. catfish	4164,25	6.46	Others	6200,33	9.13	A. catfish	13,583	21.67	Mullets	3387,2	6.91
				Mullets	3996	6.33				Others	3011,8	6.49
										Shrimp	2478,8	6.03
										G. carp	2614	5.23
Mariout	Group A			Group B			Group C
	Av. Similarity: 89.94			Av. Similarity: 92.16			Av. Similarity: 89.33
	Species	Av. Bio.	Cont.%	Species	Av. Bio.	Cont. %	Species	Av. Bio.	Cont. %
	Tilapia	2635,86	72.74	Tilapia	3099,08	58.34	Tilapia	4953,88	57.75
	A. catfish	865,43	21.7	A. catfish	2102,75	40.85	A. catfish	3449,38	39.19

). In Lake Burullus, the distinct groups identified by nMDS were primarily driven by variations in Tilapia and Mullet biomass, with Group A showing a lower average biomass compared to Group C, which exhibited the highest Tilapia biomass. Similarly, in Lake Edko, the separation of groups was mainly due to changes in Tilapia biomass. Lake Manzala’s four groups were differentiated by fluctuations in Tilapia, Mullets, and A. Catfish, with Group B showing higher overall species biomasses. Lake Mariout’s groups were primarily defined by shifts in Tilapia and A. Catfish populations. These findings align with the nMDS results, which indicate significant temporal changes in fish community structure, by pinpointing the key species responsible for these shifts and quantifying their contributions to the observed dissimilarities between time periods. This integrated approach provides a comprehensive understanding of the dynamic changes in fish communities across these lakes, linking overall community patterns to specific species-level variations.

4. Discussion

This study investigated the temporal variations in fish landings and fish community structure within the four Nile Delta lakes (Mariout, Edku, Burullus, and Manzala) from 1991 to 2019. The results revealed significant temporal shifts in fish community structure, varying trends in landings and fishing effort, and distinct patterns of CPUE across the lakes.

The observed temporal changes in fish community structure, as demonstrated by the nMDS and SIMPER analyses, highlight the dynamic nature of these ecosystems. The shifts in species assemblages, particularly in Burullus and Mariout, suggest responses to environmental pressures and management practices. The dominance of Tilapia in most lakes, coupled with fluctuations in other commercially important species like Mullets and A. Catfish, indicates potential changes in ecological balance and resource availability. By pinpointing the key species responsible for these shifts and quantifying their contributions to the observed dissimilarities between time periods, the SIMPER analysis corroborated the nMDS results, which indicated significant temporal changes in fish community structure. This integrated approach provides a comprehensive understanding of the dynamic changes in fish communities across these lakes, linking overall community patterns to specific species-level variations. Recent studies have further revealed a significant shift in fish species composition across these lakes, with a decline in rare species and a rise in adaptable ones like Catfish and Mullet, indicating biodiversity loss and ecological changes, correlated with increasing pollution levels [23]. These results, detailed in [23], were based on species’ abundances in fish landings, their ecological characteristics, and observed responses to environmental changes. Specifically, “rare species” were identified by their low abundance (e.g., GAFRD’s “other fish” category, representing 6.4% of the total landings) and observed severe decline, indicating low resilience to environmental pressures. Conversely, “adaptable” or “opportunistic” species, such as Catfish and Mullet, were categorized due to their significant increase in landings and known ability to thrive in polluted, often hypoxic conditions owing to their high environmental stress tolerance [23]. While Tilapia historically represented a large percentage of landings, the “opportunistic” designation in this context was primarily applied to the increasing trends of highly tolerant Catfish and Mullet.

The Egyptian government initiated an extensive, multi-phase “Rehabilitation of Egyptian Lakes” program. For example, the Lake Burullus project was started in February 2010. This project aimed to enhance the lake’s ecological efficiency by increasing saline water flow, deepening its basins through radial canal creation, and undertaking extensive purification operations. These comprehensive interventions have since demonstrably reshaped the lake’s fish production, species composition, and associated fishing practices, yielding both positive and nuanced impacts across its ecological and economic systems. Specifically, recent studies [29,30] indicated a significant increase in the lake’s mean annual fish production, concurrently with shifts in species dominance, notably favoring Tilapia (whose relative importance rose from 52.3% to 59.7%) while negatively affecting Catfish and, surprisingly, Grass Carp, though Mugilidae populations remained stable. Furthermore, despite official data reflecting a decrease in licensed fishing boats and fishermen—likely due to stricter enforcement—both CPUE and catch per fisherman significantly improved [29,30]. This points to enhanced economic efficiency within legal fishing practices, as evidenced by legal nets proving more profitable and resource-efficient than their illegal counterparts. Nevertheless, these macro-level economic gains have not universally translated into improved livelihoods for all fishermen, resulting in some discontent and underscoring the intricate social dimensions inherent in conservation and management initiatives [29,30]. Similarly, rehabilitation efforts undertaken in Lake Manzala, involving purification, water quality improvements, and boughaz (the inlet connecting the Lake to the Mediterranean) deepening, have similarly fostered a significant recovery and development of its fishery [31,32].

The increasing amateur fishing activity observed, particularly in Lake Manzala and Edku (since 2015—see Figure 3D), may reflect the lakes’ resilience, but also raises concerns about potential overexploitation. Lake Manzala, the largest Egyptian coastal lake, is one of the most valuable fish sources in Egypt and has been reported to contribute a large percentage of fish production from Egyptian lakes [32,33]. Lake Manzala faces significant challenges, including habitat degradation, the proliferation of aquatic plants, and severe pollution, producing an estimated (4 × 10⁹ m³) of industrial, municipal, and agricultural wastewater annually [34]. Compounding these environmental issues are human-induced problems such as illegal fishing, overharvesting, blocked boughazes (inlets), and low awareness among fishermen [33,35]. These trends suggest a shift in fishing practices, with a potential transition towards amateur and informal fishing activities. The significant decline in 1-year and 5-year fishing licenses in both Manzala and Edku, alongside the surge in amateur fishing and fishers without boats, suggests a shift towards informal and unregulated fishing practices. This trend may indicate socio-economic pressures, regulatory challenges, or changes in fishing practices. Specifically, high unemployment rates in traditional fishing communities and increasing poverty levels often compel individuals to shift towards amateur fishing and informal practices as alternative livelihoods. Concurrently, a growing local and regional demand for fish, often at lower prices, can incentivize the development of informal supply chains that bypass official monitoring and regulation. Such shifts can have profound implications for fisheries management, potentially leading to unsustainable exploitation and inaccurate data collection.

The potential for informal fishing activities also raises concerns regarding the reliability of fishing effort data, particularly in later years. Specifically, the accuracy of metrics such as the ‘number of licenses’ obtained from the GAFRD may be compromised (for more details on GAFRD’s data collection methods, refer to [24,25]). While GAFRD serves as the official and sole source of fishing effort data within the country, it remains uncertain whether the reported decline in license numbers accurately reflects actual fishing pressure. Furthermore, the impact of increasing unlicensed fishers on overall fishing effort and landings data warrants consideration. This situation underscores the need for revised data collection methodologies that incorporate informal fishing activities. Previous studies have also highlighted the presence of Illegal, Unreported, and Unregulated (IUU) activities by Egyptian vessels, even in marine fisheries and in other countries, which are more difficult to monitor than domestic fisheries [36]. Although the sampling method by GAFRD carries a risk of catch underestimation, these official data are used by international organizations such as the FAO and represent the only long-term national dataset available. Effort data, collected and updated annually at each GAFRD branch office where vessels are registered, are considered reliable, particularly regarding vessel numbers and licenses.

The observed trends also suggest a significant improvement in fishing efficiency or resource availability in Lake Manzala, along with Lake Brullus in 2018 and 2019, while the other lakes maintained relatively stable or low levels of productivity. The increased CPUE observed in Lake Manzala, contrasting with the relatively stable or low CPUE in other lakes, suggests varying levels of fishing efficiency or resource availability. This disparity could be attributed to differences in lake morphology, nutrient loading, or management interventions (such as purification projects), warranting further investigation to understand the underlying mechanisms.

The analysis of landings composition revealed distinct patterns in species dominance and diversity across the lakes. Burullus consistently showed high landings, dominated by Tilapia and Mullets, with a notable presence of European Seabass and A. Catfish, indicating a productive ecosystem but also raising questions about species dominance and potential ecological imbalances. Edku, with its low landings and Tilapia dominance, may be experiencing environmental stress or habitat degradation, as indicated by its reduced area and wastewater inflow. Lake Edku, once considered among Egypt’s most productive lakes [37], now faces significant environmental challenges, including pollution and land reclamation, which have impacted its fisheries [37]. Lake Mariout, despite historically being a vital fish source [38], has experienced a significant decline in fish production due to factors such as reclamation, overfishing, and pollution [38]. Furthermore, fishermen in Lake Mariout have specifically identified challenges related to weak fish stocks and decreased water levels, impacting the lake’s development and productivity. These decreased water levels have primarily been attributed to extensive reclamation activities for urban and agricultural expansion, the diversion of freshwater inflows from historical sources for irrigation and other human uses, and increased evaporation rates exacerbated by climate change. Manzala’s diverse catch and Mariout’s increased landings in recent years suggest varying ecological conditions and resource dynamics.

Several important insights can be drawn from the findings of this study for fisheries management and biodiversity conservation in the Nile Delta lakes. Firstly, the observed shifts in fishing practices and licensing trends necessitate a re-evaluation of current regulatory frameworks and enforcement strategies. Integrating socio-economic factors into fisheries management plans is crucial to address the challenges of informal fishing and ensure sustainable resource utilization. This could involve the establishment of co-management committees involving local fishers and stakeholders, alongside targeted training programs on sustainable fishing practices and alternative livelihoods to ensure compliance and enhance resource stewardship.

Secondly, the varying trends in CPUE and landings composition across the lakes highlight the need for lake-specific management approaches. Conducting detailed ecological assessments to understand the underlying mechanisms driving these variations is essential. Implementing adaptive management strategies that consider lake morphology, nutrient loading, and species-specific ecological roles can enhance fisheries sustainability and biodiversity conservation. Furthermore, mechanisms for balancing aquaculture and capture fisheries should be developed, such as promoting policy frameworks for integrated aquaculture capture systems (e.g., polyculture models that can reduce pressure on wild stocks), coupled with incentives for environmentally friendly aquaculture practices and the restoration of degraded natural habitats to support wild fish populations.

Thirdly, the observed temporal changes in fish community structure emphasize the importance of long-term monitoring programs. Establishing baseline data and tracking changes over time can provide valuable insights into ecosystem dynamics and inform conservation strategies. Integrating historical data with contemporary monitoring efforts can enhance our understanding of long-term trends and facilitate effective management interventions. Finally, the study’s findings contribute to a broader understanding of anthropogenic impacts on aquatic biodiversity, particularly in low- and middle-income countries where data scarcity and environmental challenges are prevalent. The results underscore the need for integrated research and management approaches that consider the complex interplay of ecological, socio-economic, and regulatory factors. This could be significantly enhanced through the implementation of modern monitoring technologies, including remote sensing techniques (e.g., satellite imagery for habitat mapping and water quality assessment) and the integration of citizen science initiatives for real-time data collection. To overcome the significant gaps in current practices, such as manual, paper-based logbooks for reporting and inefficient tracking of fishing vessels, recent studies have proposed low-cost digital workflows integrating electronic reporting with tiered vessel tracking [39]. Such an integrated system can significantly enhance data accuracy, strengthen compliance with regulations, and promote data-driven decision making for sustainable fisheries management.

This study relied on historical fisheries data, which may have inherent limitations in accuracy and completeness. While specific statistical error margins for the raw data were not provided by GAFRD, the consistency of their collection methodologies over the long time span minimized inconsistencies stemming from changes in approach. The acknowledged potential for underestimation in landings data, particularly from the sampling method, is understood to introduce a systematic bias rather than a random error. This implies that the observed trends and proportional changes in fish landings across years and species remain valid for identifying long-term ecological shifts and the impacts of management policies. Therefore, the main conclusions drawn in this study, particularly concerning shifts in community composition and responses to environmental pressures, are considered robust, as they are based on these reliable trends and relative changes, rather than absolute values. Integrating data from other sources, such as ecological surveys and socio-economic assessments, can provide a more comprehensive understanding of the studied ecosystems. Future research should focus on investigating the specific drivers of observed changes, such as water quality, habitat degradation, and climate variability. Conducting ecological modeling and scenario analyses can help predict future trends and inform management strategies.

Furthermore, investigating the socio-economic impacts of changing fishing practices and developing community-based management approaches can enhance the sustainability of fisheries resources. Incorporating local ecological knowledge and engaging stakeholders in decision-making processes can improve the effectiveness of conservation and management efforts.

In conclusion, this study provides valuable insights into the temporal dynamics of fish communities and fisheries in the Nile Delta lakes. By highlighting the impacts of anthropogenic activities and the need for adaptive management strategies, this research contributes to the ongoing efforts to conserve aquatic biodiversity and ensure the sustainable utilization of these vital ecosystems.

5. Conclusions

This study provides a comprehensive, long-term analysis (1991–2019) of the Egyptian Nile Delta lakes, revealing significant trends in fish landings, fishing effort, and community structure. Among its key contributions, this research distinctly quantifies the pronounced temporal shifts in fish community structure within each lake, as rigorously demonstrated by nMDS and SIMPER analyses. It also highlights a concerning and quantitatively discernible transition towards increased amateur and informal fishing activities, alongside a decline in formal licensing, particularly in Lake Burullus. Our findings underscore the critical role of Tilapia (Oreochromis niloticus) as a dominant species across all four lakes, particularly in Lake Burullus, which consistently demonstrated the highest productivity. We observed a concerning shift in fishing practices, with a decline in traditional licensing and a rise in amateur and informal fishing, particularly in Lake Burullus. The application of nMDS and SIMPER analyses clearly demonstrated distinct temporal shifts in fish community structure within each lake, likely driven by a combination of invasive species, pollution, and habitat degradation. These causal links were inferred from the empirical data and detailed discussions in preceding sections of this paper, which highlighted factors such as habitat alteration from reclamation and aquaculture policies, the observed proliferation of pollution-tolerant species, and documented environmental pressures on specific lakes reported in the literature (e.g., [23]).

These ecological changes, coupled with unsustainable fishing practices, highlight an urgent need for lake-specific management strategies and robust, long-term monitoring programs. The insights gained emphasize the necessity of integrating socio-economic factors into fisheries management plans, crucial for addressing the complexities of informal fishing and fostering sustainable resource utilization across the region. Such initiatives are crucial to mitigate further biodiversity loss, ensure the sustainability of these vital fisheries, and protect the ecological integrity of the Nile Delta lakes for future generations. Furthermore, the observed dynamics in these Egyptian lakes offer valuable comparative insights for other freshwater and brackish wetland ecosystems globally that are experiencing similar pressures from anthropogenic activities, such as urbanization, agricultural intensification, and climate change. Thus, this research contributes to a broader understanding of complex human–environment interactions in vulnerable aquatic systems worldwide.