The Wadi El-Rayan lakes are important aquatic environments located at the border of the great North African Sahara. Quantifying the temporal changes in these lakes due to natural and/or anthropogenic stressors is critical when assessing potential impacts on aquatic ecosystem health and the sustainability of fisheries. To detect the changes in fish communities and their drivers, the landing composition of the Wadi El-Rayan lakes over the past 30 years was quantitatively analyzed. The areas of the lakes dramatically decreased from 110 km2 in 1991 to 73 km2 in 2019. The loss of the lake area was attributed to climate warming, where the evaporation rate exceeded the volume of recharge and the recharge decreased due to an increase in agriculture and aquaculture. The total landing significantly increased in the past three decades due to an increase in the fishing effort (number of licensed boats). Nile tilapia, mullet, and grass carp dominated the landings. The pelagic-to-demersal ratio indicated a shift in the fish community composition towards demersal species. This shift was attributed to an increase in the eutrophication level. The fish communities of the landing data were clustered into four distinct groups. These clusters were significantly differentiated (p < 0.001) in both a PERMANOVA test and a PCA plot. There was a gradual replacement of the dominant species among these clusters. The most recent cluster (2018–2019) was characterized by rare species dominating the community. This shift in species composition suggests that target taxa may have been overexploited. The total landing also decreased, which may have been a result of climate warming. Furthermore, the presence of alien and warm-water species significantly increased. The fish community structure and composition shift could be attributed to anthropogenic (mismanagement) and natural climatic changes (warming).
