Methylmercury (MeHg) is a neurotoxin that poses a significant threat to aquatic ecosystems, wildlife, and human populations through seafood consumption. Microbial communities in wetlands play a crucial role in the transformation of mercury, involving the HgcAB gene for mercury (Hg) methylation and the mer operon for Hg demethylation. However, the control mechanisms governing microbial activities and Hg transformations in these ecosystems remain poorly understood. We investigated eight prairie wetland ponds with MeHg concentrations ranging from 0.085 to 3.14 ng/L and identified the microbial communities and the physicochemical factors influencing their composition. Water and sediment samples were collected from each pond and analyzed for total Hg, MeHg, chlorophyll a, dissolved organic carbon (DOC), and sulfate (SO4) concentrations, along with various water quality parameters (temperature, pH, dissolved oxygen percentage, and oxidation-reduction potential). We employed 16S rRNA gene sequencing to characterize the sediment microbial communities and used generalized linear latent variable models, principal component analysis and principal coordinate analysis to explore the associations between taxon abundances and environmental covariates.Distinct patterns in the microbial communities of the prairie wetland ponds were observed with varying MeHg concentrations. We found that microbial communities were influenced by various environmental factors such that communities in ponds with elevated DOC, SO4, and MeHg concentrations were different, taxonomically and functionally than those in ponds with lower concentrations. Our study demonstrates that some ponds exhibited similar microbial communities while others displayed differences, depending on a complex interaction between environmental factors and microbial structure. We show that community structure differs in ponds with different concentrations of MeHg, DOC and SO4, highlighting their associations with the surrounding environmental conditions. Understanding these dynamics is important for formulating effective strategies for managing MeHg contamination in these ecologically significant wetland ecosystems.