Freshwater ecosystems are globally significant sources of greenhouse gases (GHG) to the atmosphere. Generally, we assume that in-situ production of GHG in streams is limited by turbulent reaeration and high dissolved oxygen concentrations, so stream GHG flux is highest in headwater streams that are connected to their watersheds and serve as conduits for the release of terrestrially derived GHG. Low-gradient streams contain pool structures with longer residence times conducive to the in-situ production of GHG, but these streams, and the longitudinal heterogeneity therein, are seldom studied. We measured continuous ecosystem metabolism alongside concentrations and fluxes of carbon dioxide (CO₂), methane (CH₄) and nitrous oxide (N₂O) from autumn to the following spring along an eight kilometer segment of a low-gradient third order stream in the North Carolina Piedmont. We characterized spatial and temporal patterns of GHG in the context of channel geomorphology, hydrology, and ecosystem metabolic rates using linear mixed effects models. We found that stream metabolic cycling was responsible for most of the CO₂ flux over this period, and that in-channel aerobic metabolism was a primary driver of both CH₄ and N₂O fluxes as well. Long water residence times, limited reaeration, and substantial organic matter from terrestrial inputs foster conditions conducive to the in-stream accumulation of CO₂ and CH₄ from microbial respiration. Streams like this one are common in landscapes with low topographic relief, making it likely that the high contribution of instream metabolism to GHG fluxes that we observed is a widespread yet understudied behavior of many small streams.