In our previous study, we found that household chemical contaminants in indoor dust, such as cleaning agents and pharmaceuticals, can substantially alter microbial community composition and increase the abundance of antibiotic resistance genes (ARGs) and virulent pathogenic viruses. These findings suggest that chemical pollution may directly shape microbiomes and antibiotic resistance in the environment. To test this hypothesis in aquatic systems, we examined riverine particles and marine sediments. In the river study, microbial communities associated with microplastics differed from those on natural particles, and microplastics harbored higher levels of ARGs. In the sediment study, we observed that pollutant exposure markedly shifted sediment microbial community structure, altered ecosystem functioning, and that microbial community features can serve as indicators of the health status of marine benthic ecosystems. We further validated these findings using mesocosm experiments, which showed that adding organotin pollutants, such as triphenyltin and tributyltin compounds, modifies sediment microbiomes and their ecosystem functions. By constructing species sensitivity distribution curves, we derived effect thresholds to benchmark contaminant impacts and quantify the ecological risks of target pollutants. Overall, chemical contamination can restructure biological communities and impair ecosystem function and services, highlighting the importance of pollution reduction for ocean sustainability.