Freshwaters are critical to human survival and well-being. However, over-reliance on freshwaters has made them among the most threatened ecosystems in the world. Freshwaters also connect terrestrial and marine ecosystems, making them a melting pot for anthropogenic stressors, in-particular agricultural and urban runoff containing chemical and nutrient pollution. Many of the ecosystem services provided by freshwaters are directly or indirectly supported by microorganisms, which form the basal layer of aquatic food webs, drive nitrogen fixation, oxygen production, and nutrients cycling. Yet the effects of multiple interacting stressors on microbial populations and communities is poorly understood and rarely considered in policy development. Here, we evaluate the current state of knowledge around how key anthropogenic stressors, pesticide and antibiotic pollution, affect freshwater microbiomes. Based on their concentrations in EU rivers and prevalence in agriculture, we review freshwater microbial community responses to eight selected chemicals pollutants: glyphosate, diflufenican, oxytetracycline, amoxicillin, metaldehyde, imidacloprid, tebuconazole, and chlorothalonil. We focused on mesocosm-based studies as these balance environmental realism and experimental control, providing mechanistic insights into ecological effects. Our review revealed a systematic bias towards a limited selection of chemicals, studied in isolation, on a subset of microbial taxa. For example, studies focussing on glyphosate represent approximately ⅓ of all the relevant publications identified, while other prevalent chemical pollutants such as metaldehyde, chlorothalonil, and diflufenican are ignored. More research is urgently needed to fill this gap, especially studies investigating the interacting effects of chemical mixtures with other anthropogenic stressors, for example nutrient pollution and climate change. We propose a move away from the over-simplistic study of chemical pollutants towards a research agenda that incorporates more realistic scenarios and comprehensive biomonitoring combining taxonomic and trait-based information.