Methane, a common product of anaerobic carbon degradation in freshwater anoxic environments, is both a potent greenhouse gas (GHG) and a valuable bioresource. Peatlands and anaerobic digesters are useful model systems for studying anaerobic carbon degradation. In both systems, terminal electron acceptor (TEA) availability is low and community metabolism is dominated by fermentation and methanogenesis. When high-energy TEAs are available, microorganisms involved in respiratory metabolisms have a thermodynamic advantage over fermenters and methanogens competing for the same electron donors, diverting carbon flow, and disrupting community dynamics. The effect of sulfate availability on carbon flow in anaerobic digesters and peatlands is of special importance. In anaerobic digesters, sulfate can enter through waste streams and contribute to a reduction in methane through stimulating competing physiologies, while also producing corrosive effects through the production of hydrogen sulfide. In peatlands, sulfate may enter through atmospheric deposition and disrupt established carbon cycling pathways, leading to inhibition of methanogenesis, but the overall effects on carbon cycling and community stability are unclear. The studies presented here are explorations of microbial community structure and functioning in anaerobic digesters and peatlands and their responses to sulfate availability. Two studies focus on microbial communities in wastewater batch reactors (anaerobic digesters). The first evaluates changes to community structure and function in response to co-digestion with a variety of food industry wastes, with a focus on bioaugmentation cultures designed to improve start-up of co-digestion. The second study takes a detailed look at physiological responses to sulfate in a model butyrate-to-methane bioreactor using the tools of metatranscriptomics and metagenomics. Three studies focus on peatlands. The first, is a broad survey of microbial community differences between differing peat soils in the Adirondack Mountains. The second study uses a gene-centric global analysis of functional genes to identify characteristic functions of peat bogs, followed by a genome-centric case study of carbon degradation pathways in a temperate bog. The final study returns to a focus on sulfate availability as an analysis of metagenomes from two contrasting peatlands responding to sulfate. Together these studies advance our understanding of carbon flow in pristine and sulfate-impacted freshwater anoxic environments.