The present study was carried out with the purpose of monitoring the recent zooplankton and benthic macroinvertebrate assemblage and evaluating the ecological state of Wadi El-Rayan Lakes, which are solely dependent on waste and agricultural discharging water through the El-Wadi drain. The study commenced in November 2018 and ended in July 2019, during which water samples were collected to measure environmental parameters. The Shanon-Wiener diversity index (H`) and Bray-Curtiz similarity index were applied. The Biological Monitoring Working Party (BMWP) and Average Score Per Taxon (ASPT) were also applied to the upper and lower Wadi El-Rayan Lakes for the first time. In the upper lake, forty adult zooplankton taxa were identified, while in the lower lake, the number of species declined dramatically to nineteen adult species and three immature stages. Rotifera dominated the upper lake, whereas Copepoda dominated the lower lake. A total of ten macro-invertebrate taxa were identified in the upper lake, whereas thirteen were identified in the lower lake. The benthic communities of the upper lake consist of Mollusca, Annelida, and Arthropoda, while those of the lower lake comprise Arthropoda, Mollusca, Annelida, and Coelentrata. Although the upper lake displayed a poor to medium ecological status, the lower lake exhibited diverse populations, indicating a better ecological condition. The BMWP score of the upper lake was 41, suggesting a moderate status, while the lower lake's score was 59, indicating a moderate ecological status as well. The ASPT values indicated a moderate ecosystem status for both the upper and lower lakes. This study established a baseline reference for future monitoring, and calls for stakeholders to take special care of this crucial protectorate to mitigate uncontrolled activities.