The present study deals with the broader understanding of phytoplankton assemblage pattern and their ecohydrological interactions in two ecologically distinct floodplain wetlands of Teesta − Torsa basin, India. Analyses of data revealed significant seasonal variations (p ≤ 0.05) of ten water variables (temperature, transparency, pH, conductivity, total dissolved solids, dissolved oxygen, total hardness, total alkalinity, PO4 − P, and SiO4 − Si) in both the wetlands; however, no significant variation was observed among the sampling stations. In total, 128 species of phytoplankton were recorded (118 species belonging to 94 genera in seasonally open; 103 species belonging to 86 genera in closed wetland). Four algal groups, viz. Cyanophyceae, Coscinodiscophyceae, Bacillariophyceae, and Chlorophyceae, were the dominant quantitative component, remarkably influencing the total phytoplankton population in both the wetlands, contributing ~ 87% of total phytoplankton. Species Aulacoseira granulata alone contributed 12 − 41% and 8 − 34% to the total phytoplankton in the seasonally open and closed wetland, respectively, and indicated high organic load in both the wetlands. Altogether thirty-six and thirty-one phytoplankton taxa appeared as major indicators across the seasons for seasonally open and closed wetland, respectively. The indicator taxa (Aulacoseira, Oscillatoria, Dolichospermum, Spirogyra, Synedra, Nitzschia, Navicula, Euglena, Phacus) in both the wetlands hinted that the wetlands are under pollution pressure. The assemblage structure of phytoplankton was related to transparency, NO3 − N, PO4 − P, SiO4 − Si, total dissolved solids, and temperature as evident from BIO − ENV. Furthermore, the marginal test also selected similar variables (depth, transparency, conductivity, PO4 − P, SiO4 − Si) for seasonally open and the variables such as depth, conductivity, total dissolved solids, total alkalinity, and NO3 − N for the closed wetland. The study showed that the seasonal riverine connectivity greatly influences the variations in phytoplankton community in the seasonally open wetland.