Low-order streams are critical interfaces for gas exchange between surface waters and the atmosphere. In agricultural watersheds, surface waters receive substantial inputs of nutrients and organic matter from surrounding fields, creating conditions that can enhance microbial processing and fluxes of nitrous oxide, methane, and carbon dioxide. Yet, the magnitude of gas fluxes, and their spatial and temporal variability, within agricultural watersheds remains poorly constrained, as do the controls driving variability. Here, we quantify gas fluxes from low-order streams embedded within an agricultural watershed and reveal pronounced heterogeneity in emissions across space and time. Fluxes varied notably over short distances and among sampling dates, suggesting sensitivity to local biogeochemical conditions rather than uniform watershed-scale controls. This variability likely reflects interactions among hydrologic connectivity and nutrient and organic matter availability which vary at fine spatial and temporal scales. Improved characterization of when and where gas fluxes are greatest is critical for identifying management strategies that mitigate gaseous losses while retaining nutrients and organic matter on the landscape.