Zooplankton composition and abundance were investigated seasonally at ten sites in Lake Timsah and the adjacent, connected western lagoon in relation to the physicochemical conditions. A total of 42 taxa (including larval stages) were identified, among them 21 species of copepods, 6 rotifers, 5 cladocerans, 1 chaetognath and 1 urochordate. Copepods represented the predominant component (77.7% of the total community), followed by rotifers, molluscs, cladocerans and (9.2, 4.7 and 3.9% respectively), while other groups collectively formed about 4.5% of the total zooplankton population. Summer was the most productive season with an average count of 40 864 individuals m−3. The dominant copepod species were Paracalanus crassirostris and Oithona nana representing 28.3 and 24.3% of the total zooplankton respectively. The total zooplankton count, including copepods, and its dominant species showed significant positive correlations with temperature, pH and total phytoplankton density. However, negative correlations were detected between densities of rotifers, and salinity and dissolved oxygen.