Stream ecosystems exhibit high degrees of spatial heterogeneity in environmental conditions, communities of organisms, and ecosystem processes at nested scales from landscapes to microhabitats. This heterogeneity may facilitate the co-occurrence of biogeochemical processes that are favored under incompatible environmental conditions, like dinitrogen (N2 gas) fixation and denitrification. We hypothesized that environmental variation at the patch scale (1-10’s m) would facilitate the co-occurrence of N2 fixation and denitrification through the formation of ecosystem control points or patches that show high reaction rates relative to the surrounding area. We measured rates of N2 fixation and denitrification and relative abundances of the genes nifH and nirS (genes that encode for the enzymes nitrogenase and nitrite reductase respectively) in patches determined by channel geomorphic units and substrate type in seven streams encompassing a gradient of N and P concentrations. We found ecosystem control points, where rates of N2 fixation and denitrification were 1 to 4 times higher than reach-average rates (0.2 – 1400 μg m-2 h-1 and 350 – 60000 μg m-2 h-1, respectively), occurred in all study streams. Most N2 fixation control points were in patches with rock substrates, while denitrification rates and relative abundances of nifH and nirS were higher in fine sediment patches. Yet, in two of the streams, rates in the top 25% of all patches for both denitrification and N2 fixation occurred in the same patches, suggesting that variation in conditions at the sub-patch scale can also facilitate co-occurrence of these processes. Across all streams and patches, organic matter and dissolved oxygen concentrations were important predictors of rates of N2 fixation, denitrification, and nifH relative abundance, while P concentration was important to N2 fixation and denitrification. Our results demonstrate that understanding the spatial ecology of microbially-driven nutrient cycling is required to characterize nutrient fluxes more completely in stream ecosystems.