In this study, relationship between summer dynamics of chlorophyll a, nutrient, temperature, pH, salinity, dissolved oxygen, phytoplankton diversity and density are investigated in Gomishan wetland. Based on results, 5 branches of phytoplankton (13 genus and 15 species) has identified in summer. Cyanophyta and Bacillariophyta have the most phytoplankton diversity and Chlorophyta and Cyanophyta have the most cell density. At 4, 5 and 6 stations under the influence of agricultural drainage, urban and industrial wastewaters, the blooming of Cyanobacteria and Chlorophyta has occurred. The eutrophic level obtained eutrophic (mild) and hypereutrophic at these stations. Pearson correlation result shows that log Chla is significant with salinity at the level of p <0.05 and is significant with water temperature and orthophosphate at the level of p <0.01. According to the results, limited exchange of the Caspian Sea water has an effective role on environmental stress of the area that includes increased nutrient concentrations, temperature, salinity, concentration and density of the algal harmful species. To preventing harmful algal blooms, wastewater treatment from the primary pollution sources and using of aerobic stabilization ponds in the presence of resistant microalgae including chlorella, chlamydomonas and chroococcus is suggested.