Recent findings have evolved researchers’ understanding of the connections between environmental processes and production of methane (CH4) and nitrous oxide (N2O), both potent greenhouse gasses (GHGs). Production of these two gasses has traditionally been associated with anoxic sediments, but recent evidence has linked CH4 production to aquatic photosynthesis. Here, we report on the links between CH4 and N2O and lake morphology, ecosystem metabolism, and dissolved organic carbon (DOC) composition in 8 lentic water bodies (wetlands, lakes, and reservoirs) in Indiana, USA. We measured CH4 and N2O using headspace equilibration and used spectroscopy to analyze DOM composition. We used diel variation of dissolved oxygen concentrations to measure ecosystem metabolism in the form of gross primary production (GPP) and respiration (R). We found that the shallowest water bodies had the highest concentrations of CH4 and the highest rates of GPP and R. N2O was also negatively correlated to water body depth and positively correlated to R and nitrate concentrations, but not GPP. Concentrations of CH4 were also linked to DOC composition. Specifically, CH4 increased with levels of recently fixed, aquatic DOC and tryptophan-like DOC, which suggests that CH4 production may be stimulated by increasing levels of autochthonous DOC. Overall, we found that concentrations of GHGs in these lentic water bodies were linked to water body depth, GPP, and R and were not correlated to oxygen levels within or across the systems studied. Overall, aerobic processes were positively correlated to CH4 concentrations, highlighting knowledge gaps regarding the relationship between internal carbon cycling and GHG production in lentic water bodies.