Analysis of phytoplankton community structure of an aquatic ecosystem is the first priority for evaluating water quality, estimating water pollution and studying the possibility of exploiting them. In the present study, the wetlands of Mahabad, Hasanlu and Yadegarlu in West Azarbayjan were evaluated. Sampling was performed seasonally throughout the year. The total number of 94 species from five phyla (Streptophyta, Chlorophyta, Ochrophyta, Moizoa, and Cyanophyta) and 11 classes (Bacillariophyceae, Zygnematophyceae, Chlorophyceae, Cryptophyceae, Mediophyceae, eustigmatophyceae, Xanthophyceae, Dinophyceae, Chrysophyceae, Cyanophyceae, and Ulvophyceae)  was identified. The highest levels of phytoplankton diversity in these three lagoons were found in Streptophytae and Chlorophytae (59%) following by diatoms (21%) and cyanobacteria (8%), respectively. The variations of phytoplankton communities in Hasanlu (63 taxa) and Mahabad lakes (51 taxa) were quite similar. Yadegarlu Lake showed the lowest level of phytoplankton diversity (30 taxa) with different community composition which was typical for temporal wetlands in temperate zones. In Yadegarlu Lake, flagellates and cyanobacteria showed adaptive traits to extreme conditions and periods of drought by formation of resistant cysts and akinetes, respectively.