Three different locations in, Ismailia, Egypt was chosen for this study during the period from autumn 2005 to summer 2006. Blue-green algal bloom occurred during winter in Ismailia freshwater canal. Physico-chemical parameters varied among the selected freshwater, marine and brackish water bodies, chlorophyll a at all water bodies were more or less correlated with the total phytoplankton counts through the study period. Phytoplankton samples yielded a diverse array of algae including a total of 116 taxa have been identified. Most of them belong to Chlorophyceae (31); Bacillariophyceae (51); Cyanophyceae (19); Dinophyceae (12); one species of Cryptophyceae and two species belong to Euglenophyceae. The result indicated that the most important environmental variables affecting the differences and distribution of phytoplankton among the selected three different water bodies are nitrogen in the form of nitrate and ammonium which was highly correlated with the leading species of phytoplankton while PO4, salinity and water temperature are highly negatively correlated with it while lead is not affecting the phytoplankton. Other variables showed no significance correlations with the exception of chlorophyll a which had a highly negative correlation.