This work was designed to determine and assess the faunal zooplankton community structure in Lake Edku, Egypt, to explain the present status of zooplankton and water quality to assess the ecological impacts and the induced change in the zooplankton community. Zooplankton and water samples were collected seasonally. Seven sampling stations were selected to represent different habitats of the Lake that were classified in this study to three distinct habitats; Body of the lake (BL), Drainage (D) and Lake- Sea Connection (LSC). Several physical and chemical variables were studied, such as temperature, transparency, alkalinity, water pH, chlorosity, electrical conductivity, water depth, dissolved oxygen (DO), chemical oxygen demand (COD), biological oxygen demand (BOD), and water hardness. Zooplankton community consisted of 72 species dominated by three groups, Rotifera, Copepoda and Cladocera. These groups were representing 89.5%, 6.8% and 2.3% of total zooplankton density, respectively. The index of species abundance (ISA) and modified index of species abundance (MISA) showed that the small sized animals, such as Rotifera became the most dominant especially, genus Brachionus, which is considered as an indicator for organic pollution and eutrophication. Community ordination, trellis diagram and other biostatistical and multivariate analyses techniques showed that within the lake, similar ecological habitats have similar community structures for zooplankton and differ among different habitats. Comparing the present results with older data of other workers; it was appeared that zooplankton community shifted from dominance of Cladocera and large zooplankton forms to rotifers and small zooplankton by increasing eutrophication. The results of this study provide a useful knowledge about zooplankton community structure and species composition over the long term changes in the studied ecosystem.