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Flood control is one of the most important ecosystem services provided by wetlands. Large-scale loss of wetlands, combined with more intensive precipitation under changing climate, increases flood risks, to which closed watersheds are particularly susceptible. In the Devils Lake (North Dakota, USA) watershed, a prolonged wet condition since early 1990s has caused a nearly 10 m rise in water level, resulting in over $1 billion losses. While studies have shown the changing climate is the major driver of this flooding, it is still unclear how much contribution could be due to the historical conversion of wetlands in the upper basin. We developed a Soil and Water Assessment Tool (SWAT) model for the Devils Lake watershed and simulated various scenarios representing present and possible past and future wetland area. We estimated the changes in flood risks under the historical and CMIP-5 future climates with these wetland scenarios. We found that while currently wetland restoration does not significantly change flood risks, under the modified climate it presents a good complementary measure reducing the negative impacts of current flood management strategies.