Small, isolated wetlands in the Prairie Pothole Region of North America may be of critical importance to migrating shorebirds but are at high risk of drainage for agricultural production. We evaluated shorebird use of 1,181 temporary and seasonal wetlands within agricultural fields in the Drift Prairie physiographic region of North Dakota, USA over a 10-week period in spring of 2001. A total of 4,050 shorebirds of 25 species was observed on sampled wetlands. Shorebirds selected temporary wetlands that had water present during multiple visits, little emergent vegetation, large perimeters, and other wetlands in the surrounding landscape. Shorebirds were less likely to use wetlands showing evidence of drainage. Observed use of wetland basins suggests that small wetlands in the Prairie Pothole Region host millions of migrant shorebirds each spring. Continued existence of many of these wetlands may be threatened by a recent U.S. Supreme Court ruling that removed federal protection from certain isolated wetlands. Our results show the importance of current wetland protection provisions such as “Swampbuster” and other conservation practices of the United States Department of Agriculture Farm Program.