Benthic microbial communities play fundamental roles in wetland ecosystems including nutrient and energy cycling, and the degradation and assimilation of pollutants. Because of these crucial roles, along with their short-life cycles and high diversity, microorganisms can also play an important role as indicators of environmental change, which is particularly relevant in the current climate of increasing anthropogenic stressors, including factors such as emerging pollutants and climate change. Consequently, understanding the responses of microbes to environmental change is critical. To assess the effects of anthropogenic stressors on microbial communities in wetland ecosystems, I examined the response of sediment microorganisms from North Dakota wetlands in both microcosm and field-scale studies. First, I used 16S rRNA gene sequencing to analyze wetland microbial community responses to glyphosate treatments using an experimental microcosm approach. I found no significant differences in microbial communities among concentrations or treatments compared to controls, suggesting microorganisms in this region may have evolved glyphosate tolerance. Second, also taking an experimental approach, I measured methane, carbon dioxide, and nitrous oxide flux and porewater concentrations in microcosms to analyze net microbial production and consumption of greenhouse gases following glyphosate and/or 2,4-D treatment. I found high glyphosate concentrations significantly increased carbon dioxide emissions potentially due to increased microbial activity from the use of glyphosate as a substrate, or due to increased respiration as a stress response. Lastly, I used 16S rRNA gene sequencing to compare microbial communities in natural and restored wetlands across the North Dakota Prairie Pothole Region to assess the effects of a physical stressor, hydrologic restoration. I found no significant differences in microbial communities across wetlands, which may be due to the lack of direct sediment disturbance from restoration, or due to the ability of microorganisms to rapidly recover, thus showing no assemblage differences 25 years after restoration. Overall, I demonstrated that integrating microbial ecology with ecotoxicology and restoration ecology can be a beneficial and applicable research approach to understanding the impact of anthropogenic-induced environmental change on wetlands and show that the use of microbial metrics and mechanisms can provide valuable insight on pertinent issues of global concern.