Wetland catchments are major ecosystems in the Prairie Pothole Region (PPR) and play an important role in greenhouse gases (GHG) flux. However, there is limited information regarding effects of land-use on GHG fluxes from these wetland systems. We examined the effects of grazing and haying, two common land-use practices in the region, on GHG fluxes from wetland catchments during 2007 and 2008. Fluxes of methane (CH4), nitrous oxide (N2O), and carbon dioxide (CO2), along with soil water content and temperature, were measured along a topographic gradient every other week during the growing season near Ipswich, SD, USA. Closed, opaque chambers were used to measure fluxes of soil and plant respiration from native sod catchments that were grazed or left idle, and from recently restored catchments which were seeded with native plant species; half of these catchments were hayed once during the growing season. Catchments were adjacent to each other and had similar soils, soil nitrogen and organic carbon content, precipitation, and vegetation. When compared with idle catchments, grazing as a land-use had little effect on GHG fluxes. Likewise, haying had little effect on fluxes of CH4 and N2O compared with non-hayed catchments. Haying, however, did have a significant effect on combined soil and vegetative CO2 flux in restored wetland catchments owing to the immediate and comprehensive effect haying has on plant productivity. This study also examined soil conditions that affect GHG fluxes and provides cumulative annual estimates of GHG fluxes from wetland catchment in the PPR.