Soil microorganisms mediate biogeochemical processes, but how microbial community composition influences these processes remains contested. We combined monthly sequencing of soil 16S rRNA genes and intensive measurements of nitrogen (N), carbon (C), and iron (Fe) cycling along a topographic gradient in a poorly drained intensive agricultural ecosystem (corn–soybean rotation) in the midwestern United States. Observed microbial composition changed little over time within and among years despite large differences in weather and crop type. Yet, microbial composition varied greatly with topographic location and correlated strongly with moisture, soil organic carbon (SOC), and especially pH. Microbial families, genera, and/or amplicon sequence variants often correlated significantly with measured biogeochemical processes or pools, yet different taxa within the same phylogenetic groups often responded in opposite ways, indicating a lack of ecological coherence among close relatives. Dominant phyla were generally similar across the topographic gradient but specific members showed consistent tradeoffs among locations. Ammonia oxidizing archaea and bacteria sequences varied oppositely with pH across the gradient, but their combined relative abundances remained similar, as did potential nitrification rates. Nitrospira sequences correlated positively with nitrous oxide (N2O) fluxes, suggesting a direct or indirect contribution of nitrification (or possibly comammox) to N2O production. We also found significant linkages between taxonomic groups and redox-sensitive Fe pools, indicating a role for redox variation in structuring microbial communities. Several globally dominant bacteria identified previously correlated significantly with measured biogeochemical variables, providing insights into their possible functional roles. Overall, microbial composition provided a coarse measure of several key biogeochemical functions and implicated taxa that possibly mediate these processes in a widespread agroecosystem of North America.