El-Manzala Lake represents one of the most economical and valuable fish sources lakes in Egypt. This study aims to study the impact of physical and chemical properties of water on phytoplankton communities in North El-Manzala Lake. The number and biomass of phytoplankton, as well as physicochemical characteristics of surface water at the seven sites (Al-Baghdadi, Shatta, El-Deiba, Abo El-Ross, El Nafft, Towall Ibrahim, and Shatt Greba) representing North El-Manzala Lake—Damietta, Egypt, were studied from January to December 2017. Physicochemical properties of water exhibited seasonal and local variations. Phytoplankton standing crop in North El-Manzala Lake—Damietta, Egypt, was varied in relation with water quality as follows: Al-Baghdadi > El Nafft > Shatt Greba > Shatta > El-Deiba > Towall Ibrahim > Abo El-Ross. Cyanophyta was the dominant class at all sites except at Al-Baghdadi and Towall Ibrahim where Bacillariophyta and Pyrrophyta were the predominant phytoplanktonic groups, respectively. The maximum crop density was recorded in winter, whereas the lowest values occurred in summer. Pearson’s correlation coefficient revealed that most of the phytoplankton groups were significantly correlated with water temperature, pH, total alkalinity, ammonia, nitrate, silica, and ortho-phosphorus.