A one-year seasonal study was carried out to estimate the algal population and its biochemical contents in Lake Qarun in Egypt. Twelve samples representing Lake Qarun and two drains (El-Bats and El-Wadi) were examined.  Bacillariophyta was the most dominant in phytoplankton assemblages. The highest seasonal phytoplankton density was recorded during summer, whereas the lowest was in autumn. The lowest spatial phytoplankton density, chlorophyll (a), and carotenoid concentrations were recorded in drains. ANOVA revealed significant differences between seasons and stations in the density of phytoplankton species, protein, carbohydrate, and lipid. Principal component analysis (PCA) results showed that water temperature was positively correlated with Ochrophyta, Cyanobacteria, Cryptophyta and some dominant phytoplankton species, meanwhile; water temperature was negatively correlated with Bacillariophyta, some dominant phytoplankton species, Chl (a), carotenoid, protein, carbohydrate, and lipid. Hence, water temperature and nutrients (NO₃ and PO₄), drained into the lake, play a major role in the trophic state changes of Lake Qarun, and its effect on the phytoplankton community and other environmental conditions was detected during the seasons of the year.