Hydrologic margins of wetlands are narrow, transient zones between inundated and dry areas. As water levels fluctuate, the dynamic hydrology at margins may impact wetland greenhouse gas (GHG) fluxes that are sensitive to soil saturation. The Prairie Pothole Region of North America consists of millions of seasonally-ponded wetlands that are ideal for studying hydrologic transition states. Using a long-term GHG database with biweekly flux measurements from 88 seasonal wetlands, we categorized each sample event into wet to wet (W→W), dry to wet (D→W), dry to dry (D→D), or wet to dry (W→D) hydrologic states based on the presence or absence of ponded water from the previous and current event. Fluxes of methane were 5-times lower in the D→W compared to W→W states, indicating a lag ‘ramp-up’ period following ponding. Nitrous oxide fluxes were highest in the W→D state and accounted for 20% of total emissions despite accounting for only 5.2% of wetland surface area during the growing season. Fluxes of carbon dioxide were unaffected by transitions, indicating a rapid acclimation to current conditions by respiring organisms. Results of this study highlight how seasonal drying and re-wetting impact GHGs and demonstrate the importance of hydrologic transitions on total wetland GHG balance.