Contrasting fish and phytoplankton community structure along a seasonally dynamic regulated Afro-tropical river

River regulation alters environmental conditions and hydrological connectivity, yet these influences are embedded within natural longitudinal and seasonal variation. We examined fish and phytoplankton community structure across 15 sites along the Lower Niger River, regulated by two dams, during dry and rainy seasons. We evaluated compositional differences among upstream, inter-dam and downstream sections, partitioned taxonomic β-diversity into turnover and nestedness, and assessed environmental, spatial and dam associated positional contributions to community variation. Both assemblages differed among river sections defined by their position relative to the dams, although differentiation was stronger for phytoplankton. Taxonomic β-diversity was consistently dominated by species turnover, accounting for approximately 90% of fish and 72–74% of phytoplankton β-diversity. Fish showed weak correspondence with measured environmental, spatial and fragmentation gradients, despite stronger compositional differentiation during the rainy season. Phytoplankton showed stronger environmental and dam-associated spatial structuring, with dam separation being particularly important during the rainy season. Environmental, spatial and dam-associated positional components were strongly shared, particularly for rainy-season phytoplankton community composition, showing that these components are closely intertwined along the regulated river continuum. Overall, community structure reflected high taxonomic replacement and assemblage-specific responses to interconnected environmental, spatial and river-regulation-associated patterns, with actively dispersing fish showing weaker structuring than the smaller, passively dispersed phytoplankton. This contrast emphasizes the value of considering multiple biological groups with different dispersal characteristics when assessing biodiversity patterns in regulated tropical rivers.