Global rivers, particularly those in populated urban areas, are challenged by multiple stressors such as pollution from anthropogenic activities. Dissecting the relative role of each ecological process involved in structuring biotic communities is fundamental in both theoretical and applied ecology. The ecological niche-based species sorting and stochastic dynamics-based dispersal are two major competing processes in determining community structure. Studies have reached a common realization on the environmental gradient-geographical scale relationship (EGGSR), resulting in species sorting over dispersal in determining community structure at large geographical scales where significant environmental gradients often exist. However, this relationship has been recently challenged at fine geographical scales when significant environmental gradients are formed by local anthropogenic activities. Here, we used three receiving rivers of wastewater treatment plants (WWTPs) as the promising system to test the hypothesis that species sorting plays a dominant role over dispersal in structuring zooplankton communities at microgeographical scales (∼1.2 km). After WWTP effluent discharge, we consistently detected significant environmental changes in all three receiving rivers, leading to significant variation in both community structure and taxonomic co-occurrence networks. Variation partitioning showed that environmental variables explained higher proportions of community variation than spatial ones, supporting that species sorting played a dominant role over dispersal in structuring zooplankton communities. Thus, our findings here reject EGGSR, illustrating that the effect of species sorting has been overlooked in disturbed aquatic ecosystems at fine spatial scales. More importantly, all analyses in multiple rivers here validate the “microscale species sorting” hypothesis. The validation of such hypothesis provides a novel methodology for point source pollution management by assessing environment-community interactions and functional changes of biological communities. The differed variables underlying species sorting among three rivers illustrate that ecological management should be case-specific, with the full consideration of local water quality background and pollutant composition of each point pollution source.