The River Ganga is reeling from pressures of rapid urbanization and resulting anthropogenic forcings. In this study, phytoplankton community assemblages were deduced from the Dakshineswar site located in the lower stretch of River Ganga to understand the health of this river. Surface water samples were collected from six stations of Dakshineswar spanning across monsoon and post-monsoon seasons of 2019 and 2020. Stations were categorized into point source and surface water based on proximity to municipal discharges. Measurement of in situ environmental parameters showed significant differences in dissolved oxygen, total dissolved solids, electrical conductivity and suspended particulate matter between the two seasons during the study period. In particular, concentrations of dissolved nitrate and silicate were found to be higher in point source stations compared to surface water stations. The concentration of Chlorophyll-a (Chl-a) was found to be higher in post-monsoon compared to monsoon seasons. Phytoplankton communities consisted of 23 diatom taxa and 14 green algal taxa and they showed distinct seasonal and spatial variations in the study site. Phytoplankton communities were dominated by diatom taxa namely Aulacoseira, Bacillaria, Coscinodiscus, and green algal taxa such as Ulothrix, Chlorella, and Scenedesmus. There was a dramatic increase in cell abundance of Aulacoseira spp. in post-monsoon seasons indicating a bloom-like scenario. Moreover, the rapid increase in cell abundance of Aulacoseira spp. also coincided with an increase in Chl-a and a sharp fall in the concentration of dissolved silicate. Some of the encountered phytoplankton taxa such as Tetraedron, Cosmarium, Nitzschia and Scenedesmus showed strong co-occurrence patterns indicating possible association at ecological scales. Four distinct clusters were formed by nMDS ordination plot based on the influences of environmental variables on encountered phytoplankton taxa. Network analysis revealed evidence of co-occurrence patterns between several diatoms and green algal taxa.