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Abstract Headwater wetlands are important sites for carbon storage and emissions. While local- and landscape-scale factors are known to influence wetland carbon biogeochemistry, the spatial and temporal heterogeneity of these factors limits our predictive understanding of wetland carbon dynamics. To address this issue, we examined relationships between carbon dioxide (CO₂) and methane (CH₄) concentrations with wetland hydrogeomorphology, water level, and biogeochemical conditions. We sampled water chemistry and dissolved gases (CO₂and CH₄) and monitored continuous water level at 20 wetlands and co-located upland wells in the Delmarva Peninsula, Maryland, every 1–3 months for 2 years. We also obtained wetland hydrogeomorphologic metrics at maximum inundation (area, perimeter, and volume). Wetlands in our study were supersaturated with CO₂(mean = 315 μM) and CH₄(mean = 15 μM), highlighting their potential role as carbon sources to the atmosphere. Spatial and temporal variability in CO₂and CH₄concentrations was high, particularly for CH₄, and both gases were more spatially variable than temporally. We found that groundwater is a potential source of CO₂in wetlands and CO₂decreases with increased water level. In contrast, CH₄concentrations appear to be related to substrate and nutrient availability and to drying patterns over a longer temporal scale. At the landscape scale, wetlands with higher perimeter:area ratios and wetlands with higher height above the nearest drainage had higher CO₂and CH₄concentrations. Understanding the variability of CO₂and CH₄in wetlands, and how these might change with changing environmental conditions and across different wetland types, is critical to understanding the current and future role of wetlands in the global carbon cycle.