Urban rivers rely on intricate multitrophic interactions in food webs, which are vital for ecological functions. Human-induced pollutant discharge, notably micropollutants, poses a threat to these interactions. To study the impact of micropollutants on the microbial food web, we sampled downstream areas of the Jiulong River’s north tributary (lower urbanization, ∼25% built land) and west tributary (higher urbanization, ∼65% built land) for eleven consecutive days in both dry and wet seasons in Fujian, China. We constructed a conceptualized planktonic food web model by employing DNA metabarcoding targeting bacteria, micro-eukaryotes (algae and protozoa), and microzooplankton. Our results revealed that the more urbanized west tributary exhibited significantly higher micropollutant concentrations. Structural equation modeling (SEM) incorporating micropollutants and all food web elements indicated a significantly stronger impact of micropollutants on the planktonic food web in the west tributary than in the north tributary. Micropollutants exhibited both direct and indirect (cascade) effects on high trophic levels (protozoa and microzooplankton), with algal communities mediating the cascade effects instead of bacterial communities, likely due to the increased eutrophication in the urbanized tributary. Overall, our study underscores the potential ecological disruptions caused by micropollutants in shaping planktonic food web interactions in urban rivers.SynopsisUrban rivers face ecological threats from micropollutants. This study shows elevated micropollutants significantly affected the planktonic food webs. Algal, rather than bacterial, food web pathway mediated micropollutants cascading effects on high trophic levels, emphasizing micropollutant-induced disruptions in urban rivers.