The millions of wetlands that define the Prairie Pothole Region (PPR) harbor large proportions of continental populations of several species of North American waterfowl, waterbirds, and shorebirds. The PPR also has some of the highest wind energy potential in the United States of America. Thousands of wind turbines are being erected in the PPR to produce electricity and have the potential to affect migratory bird populations through collisions, displacement, barriers to movement, habitat fragmentation, and habitat loss. We assessed occurrence of waterbirds and shorebirds from 2008 through 2010 on wetlands in two wind energy development sites, defined as wetlands within 805 m of a wind turbine, and two reference sites in the PPR of North and South Dakota. We conducted 10,321 wetland visits on 3,542 individual wetland basins and related bird occurrence to wetland characteristics, upland characteristics, survey type (roadside vs. off-road), seasonal timing of sampling, year of sampling, and site type (wind energy development vs. reference). Models characterizing occurrence of Willet (Catoptrophorus semipalmatus), Marbled Godwit (Limosa fedoa), Wilson's Phalarope (Phalaropus tricolor) and Black Tern (Chlidonias niger) indicated that occurrence varied with wetland characteristics and among sites and years, was not substantially reduced on either wind energy site, but was slightly and consistently lower on one of the wind energy sites for the three shorebird species. Our results suggest that wetlands have conservation value for these species when wind turbines are present, but additional sampling across time and space will be necessary to understand the effects of wind turbines on shorebird and waterbird presence, density, survival, and reproductive success.