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Abstract The heterogeneity of carbon dioxide (CO₂) and methane (CH₄) sources within and across watersheds presents a challenge to understanding the contributions of different ecosystem patch types to stream corridor and watershed carbon cycling. Changing hydrologic connections between corridor patches (e.g., streams, vernal pools, hillslopes) can influence stream corridor greenhouse gas emissions, but the spatiotemporal dynamics of emissions within and among corridor patches are not well‐quantified. To identify patterns and sources of carbon emissions across stream corridors, we measured gas concentrations and fluxes over two summers at Coweeta Hydrologic Laboratory, NC. We sampled CO₂and CH₄along four stream channels (including flowing and dry reaches), adjacent vernal pools, and riparian hillslopes. Stream CO₂and CH₄emissions were spatially heterogeneous. All streams were sources of CO₂to the atmosphere (median = 97.2 mmol m⁻²d⁻¹) but were sources or sinks of CH₄depending on location (−0.19 to 4.57 mmol m⁻²d⁻¹). CO₂emissions were lower during the drier of two sampling years but were stable from month to month in the drier summer. CO₂and CH₄emissions also varied by both corridor and patch type; the presence of a vernal pool in the corridor had the strongest impact on emissions. Vernal pool patches emitted more CO₂and CH₄(246 and 1.95 mmol m⁻²d⁻¹, respectively) than their adjacent streams. High resolution sampling of carbon fluxes from patches within and among stream corridors improves our understanding of the connections between terrestrial, riparian, and aquatic zones in a watershed and their contributions to overall catchment carbon emissions.