Urban plain river networks often suffer from ecosystem impairment due to sluggish hydrodynamics and insufficient water replenishment. This study assessed the aquatic ecosystem of the Yunxi area in Hangzhou, a river network characterized by insufficient hydrodynamics. A systematic ecological survey of phytoplankton, zooplankton, and macrobenthic communities was conducted at 11 key sites, and their potential driving mechanisms were explored by integrating physicochemical water analysis with redundancy analysis (RDA). The results indicate generally weak hydrodynamic conditions and elevated nitrogen concentrations at several sampling sites. The aquatic biological communities were characterized by relatively high abundances of several pollution-tolerant taxa, mainly including Bacillariophyta, Rotifera, Oligochaeta, and Gastropoda. Furthermore, local dominance of Cyanophyta and Cryptophyta at specific sites indicate spatial variation in community composition. RDA further indicated that organic pollution and nutrient enrichment were closely associated with variations in aquatic community composition. According to the observed community patterns, the weak water exchange combined with nutrient and organic-matter enrichment may be associated with variations in the aquatic community composition. Therefore, targeted ecological water supplementation might be useful to enhance the regional hydrodynamic conditions, increase water exchange and reduce pollutant accumulation.