The effect of micropollutant discharges from increased river urbanization could disrupt planktonic food webs; however, the extent to which micropollutants impact these webs remains unstudied. In this study, downstream areas of the north and west tributaries of the Jiulong River (Fujian, China), which differ in their urbanization status (north: ∼25 % built land area; west: ∼65 %), were sampled for eleven consecutive days during both dry and wet seasons. We quantified micropollutant compounds and constructed a planktonic food web consisting of bacteria, algae, protozoa, and microzooplankton using DNA metabarcoding. Significantly higher concentrations of nutrients and micropollutants were detected in the more urbanized west tributary than in the north tributary. Structural equation modeling showed that the food webs in both tributaries were similarly affected by physico-chemical factors. However, micropollutants exerted a stronger influence on the food web in the west tributary than in the north tributary. Both direct and indirect effects of micropollutants on the planktonic food webs were identified in the west tributary. More importantly, the indirect (cascade) effect of micropollutants on consumers in the food web (protozoa and microzooplankton) was mediated by algae, not bacterial communities.