The Northern Great Plains (NGP) contains much of the remaining temperate grasslands, an ecosystem that is one of the most converted and least protected in the world. Within the NGP, the Prairie Pothole Region (PPR) provides important habitat for >50% of North America's breeding waterfowl and many species of shorebirds, waterbirds, and grassland songbirds. This region also has high wind energy potential, but the effects of wind energy developments on migratory and resident bird and bat populations in the NGP remains understudied. This is troubling considering >2,200 wind turbines are actively generating power in the region and numerous wind energy projects have been proposed for development in the future. Our objectives were to estimate avian and bat fatality rates for wind turbines situated in cropland‐ and grassland‐dominated landscapes, document species at high risk to direct mortality, and assess the influence of habitat variables on waterfowl mortality at 2 wind farms in the NGP. From 10 March to 7 June 2013–2014, we completed 2,398 searches around turbines for carcasses at the Tatanka Wind Farm (TAWF) and the Edgeley‐Kulm Wind Farm (EKWF) in South Dakota and North Dakota. During spring, we found 92 turbine‐related mortalities comprising 33 species and documented a greater diversity of species (n = 30) killed at TAWF (predominately grassland) than at EKWF (n = 9; predominately agricultural fields). After accounting for detection rates, we estimated spring mortality of 1.86 (SE = 0.22) deaths/megawatt (MW) at TAWF and 2.55 (SE = 0.51) deaths/MW at EKWF. Waterfowl spring (Mar–Jun) fatality rates were 0.79 (SE = 0.11) and 0.91 (SE = 0.10) deaths/MW at TAWF and EKWF, respectively. Our results suggest that future wind facility siting decisions consider avoiding grassland habitats and locate turbines in pre‐existing fragmented and converted habitat outside of high densities of breeding waterfowl and major migration corridors.