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The footprints of microplastics in the water bodies of urban agglomerations are largely dominated by superimposed anthropogenic influences. Understanding these influences and how they are correlated is essential to better understand the occurrence and variability of microplastics in different ecosystems. This study longitudinally assessed the abundance and distribution of microplastics in the water bodies of urban agglomerations at the watershed-scale in Shanghai Megacity. Particularly, the behavior of microplastics with the impacts of drainage system overflow in wet weather (WWF), land uses, and environmental management practices were explored. WWF can greatly aggravate microplastic pollution in aquatic environments. A systemic estimation based on detailed data was used to show that the annual load of microplastics discharged via WWF in the watershed area was 8.50 × 1014 p/year, which was approximately six times larger than that discharged via the local Wastewater Treatment Plant effluent. Findings here contribute to research concerning the spatial variability of aquatic microplastics and the extent to which they are affected by land use. In descending order, the highest microplastic concentrations were found in heavy industrial > commercial/public/recreational > agricultural/light industrial > agricultural > and residential areas. The longitudinal pattern of microplastics observed in the water bodies suggested that there were superimposed effects of land use and hydrodynamics. This paper is the first to provide an integrated framework that demonstrates the significant role of environmental management practices in controlling the production and transmission of microplastics to receiving waters at a city-scale. Improved management of WWF might be a tangible solution that would help achieve an immediate and large-scale reduction of microplastics in sewage. Determining the optimized management practices for different weather or hydrological conditions could be an essential factor in decreasing microplastic concentrations and altering their flow-path pattern in a given region.