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In tidal marshes, spatial and temporal variability in the importance of microbial metabolic pathways influences ecosystem-level processes such as soil carbon storage, the regeneration of inorganic nutrients, and the production of atmospherically important trace gases. We measured seasonal changes in rates of microbial Fe(III) reduction, sulfate reduction, and methanogenesis in tidal freshwater and brackish marshes on the Patuxent River, Maryland, USA, and assessed the ability of plant roots to influence these processes by regenerating electron acceptors and supplying electron donors. In both marshes, the importance of microbial Fe(III) reduction was greatest early in the summer and decreased through the study period. Coincident with the seasonal decline in Fe(III) reduction, methanogenesis (freshwater marsh) or sulfate reduction (brackish site) increased in importance. At the brackish marsh, the partitioning of anaerobic carbon metabolism between Fe(III) reduction and sulfate reduction was similar within and below the root zone, suggesting that rhizosphere processes did not control anaerobic metabolism at this site. Instead, seasonal biogeochemical patterns at the brackish marsh were affected by factors such as water table depth and iron–sulfur interactions. At the tidal freshwater site, our results suggest that changes in rates of Fe(III) reduction and methanogenesis were directly affected by plant-mediated processes. In midsummer, Fe(III) reduction accounted for a greater fraction of total anaerobic metabolism in rhizosphere-influenced surface soils than in soils below the root zone. High rates of Fe(III) reduction occurred at the expense of methanogenesis. This study documented strong temporal variations in the outcome of microbial competition for electron donors that ultimately affected the balance between Fe(III) reduction and methanogenesis within tidal freshwater marsh soils. Our data suggested that variations in microbial metabolic pathways were regulated by physiochemical factors at the brackish site and plant activity at the freshwater site. Plant regulation of Fe(III) reduction is a largely unstudied mechanism by which plants influence wetland carbon cycling and greenhouse gas production.