Freshwater systems are affected by anthropogenic factors, leading to substantial shifts in the water quality and ecological state. Chemical pollutants are a major contributor to these shifts and recent studies have shown their role in reducing water quality and altering biodiversity. The biological monitoring of freshwaters has largely excluded microbial communities, who make up most of the biodiversity, and have been shown to drive important ecosystem processes which include chemical biotransformation. While the importance of characterising changes in microbial diversity, due to pollution, is regarded to be key for monitoring ecosystem change there is a substantial knowledge deficit on the responses of microbes to environmental change brought about by chemical pollution. There are clear gaps in the links between shifts in microbial diversity and functionality that drive ecological processes such as carbon and nitrogen cycling. This knowledge deficit is even more pronounced in terms of determining the effects of chemicals in freshwater, and consequently identifying microorganisms that could serve as indicators of change, or microbial bioindicators, of specific chemical stressors from their taxonomic and functional diversity. Given the known metabolic versatility and their potential as sentinels of change, the lack of integration of microbial community data when determining biological indicators of change in water quality assessments and monitoring is somewhat surprising. This systematic review examines the contemporary literature regarding microbial community responses to aquatic pollutants such as micropollutants, excess nutrients, and heavy metals in aquatic systems. We evaluate the challenges and opportunities from the potential inclusion of microbiome analyses in biological monitoring efforts, specifically for the analysis of aquatic water quality monitoring.