Abstract: Phytoplankton and microbiological analysis of three different sites of each of El-Manzala Lake Water and Rashid branch of the River Nile of Egypt were examined. The results were compared and correlated with each other and with certain physico-chemical parameters using MVSP Ver. 3.1 program for Canonical Corresponding Analysis (CCA). Chlorophyceae and Bacillariophyceae represented 47.6 and 45.9% of the total phytoplankton in El-Manzala Lake Water, which was more, polluted than Rashid estuary water. Chlorophyceae was predominant (51.7%) in Rashid estuary water. Heterotrophic plate counts and indicators of faecal contamination were higher in El-Manzala than in Rashid water whereas both halophilic and halotolerant bacteria were higher at Rashid than El-Manzala locations. Thermophilic and/or thermotolerant fungi and bacteria were more abundant in El-Manzala water than in Rashid water.