<p>Ten surface water samples were collected from five distinct aquatic environments; the Mediterranean Sea, Estuary, Barge Canal, Nile River and Manzala Lake. Each water body possesses unique ecological characteristics. Zooplankton communities were analyzed across these environments to assess biodiversity and eutrophication status. Results revealed that trophic conditions varied significantly according to the type of water body. Mesotrophic conditions dominated the central part of the study area around the Nile River, while eutrophic conditions prevailed in the southeastern region near Manzala Lake. A total of 23 zooplankton species were recorded and classified into seven major groups. The Mediterranean Sea exhibited the highest biodiversity (11 species), whereas the Barge Canal had the lowest (4 species). Manzala Lake showed the highest standing crop (29520 org/m³), reflecting its nutrient-rich and highly productive environment influenced by agricultural and industrial discharges. This elevated nutrient input promotes marine enrichment and enhances zooplankton diversity, particularly of brackish and euryhaline species. Crustaceans dominated the Mediterranean Sea, highlighting their importance in the marine food web, while meroplanktonic larvae were predominant in the Barge Canal, indicating its function as a spawning zone for benthic organisms. Crustaceans and meroplankton were also dominant in the Nile Delta coastal area and Manzala Lake, reflecting favorable conditions for brackish water communities. Rotifers were the most prevalent group in the Nile River, indicating potential eutrophication and anthropogenic pressure.</p>