The drains of Lake Manzala play important role in the distribution of zooplankton, especially at the southeastern part of the lake. Samples were collected from six stations at southeastern sector of the lake from August, 2009 to May, 2010. Physico-chemical parameters and zooplankton were analyzed following APHA (1992). Six groups of zooplankton were recorded; Rotifera constituted the main dominant group in the lake contributing 80.04 % of the total zooplankton population followed by Copepoda (17.29 %), Protozoa (1.35%) and Cladocera (1 %). Ostracoda and Nematoda were the less dominant groups forming 0.20 and 0.12% respectively. The Highest density of zooplankton was recorded at Ibn Salam Station (4519665 Org./m3) during spring due to the effect of wastewater discharge, rich in nutrients, through 3 main drains at this area, while the lowest abundance was recorded at El-Qaboti Station (17666 Org./m3) during winter. The lowest average numbers of total zooplankton was recorded at Bahr El-Bakar Station (160840 Org./m3). This due is to discharging sewage from Bahr El-Bakar drain which considered the main source of pollution in the lake.