Biogeochemical cycles in aquatic systems are largely controlled by single cell microbes that carry out oxidation-reduction reactions either to generate energy or to convert compounds to biologically accessible oxidation states. These transformations are key to regulating availability of nutrients that limit growth and primary productivity, but the rates of these transformations and the microbes responsible for them are not well characterized, especially in large freshwater systems. In order to understand biogeochemical transformations and the microbes responsible for them in the Laurentian Great Lakes, we surveyed microbial communities using amplicon and whole community sequencing, and stable isotope probing to determine rates of nitrogen oxidation.First, we used amplicon and whole community sequencing to survey the taxonomic identity and metabolism of nitrogen oxidizing microbes (nitrifiers) in the Laurentian Great Lakes. Show that taxonomic composition of nitrifier communities was distinct across lakes, with nitrite oxidizers showing particularly dynamic distribution potentially related to substrate availability. We demonstrate that nitrifiers in the Great Lakes have streamlined genomes as compared to soil relatives, and contain metabolic adaptations that allow for access to organic nitrogen sources. We find ammonia oxidizing bacteria strains with adaptations to photic environments including proteorhodopsin, a novel protein in nitrifiers which may suggest the ability to generate energy from light. These results suggest specific adaptations to this large freshwater ecosystem, and highlight the potential importance of organic nitrogen to nitrification in the Great Lakes. Next, we employed stable isotope tracer methods to measure rates of nitrification, along with further whole community sequencing. We found that Lake Erie was distinct from the other Great Lakes in many respects. Rates of nitrification were up to an order of magnitude higher, importance of urea relative to ammonium was considerably lower, and nitrification is in some cases associated with a larger size fraction. Consistent with this, we find that the genomic identity of nitrifiers in Lake Erie are distinct from the other Great Lakes. Together this work confirms predictions made using previous whole community DNA sequencing, and established Lake Erie as a distinct biogeochemical regime with respect to nitrogen cycling. Finally, we employed whole community DNA sequencing to survey the taxonomy and metabolism of autotrophs in the Great Lakes. We discovered a surprising number of carbon fixation genes associated with order Burkholderiales, and this taxonomic group contributed the majority of carbon fixation genes in the surface and deep chlorophyll layer of most of the Great Lakes. We reconstruct the metabolism of these microbes which demonstrates that these carbon fixation genes are associated with microbes that also contain sulfur oxidation and anoxygenic aerobic phototrophy genes. We further demonstrate that carbon fixation genes and organization of the carbon fixation operon is not congruent with the overall genome phylogeny, suggesting multiple acquisitions of carbon fixation genes. Overall these results emphasize the potential importance of chemoautotrophs to organic carbon inventories, and highlight the need for measurement of dark carbon fixation in the Great Lakes.