Repairs to legal drains in the United States may be regulated to protect adjacent wetlands under Section 404 of the Federal Water Pollution Control Act, commonly known as the Clean Water Act (CWA). However, few studies have examined effects of legal drain clean-outs on adjacent wetlands and associated migratory waterbird populations. I compare water regimes, cover-to-open water ratios, and waterbird use on Bruns, Big, Meszaros, and Kraft sloughs (BBMK) in Sargent County, North Dakota before and after the clean-out of Crete-Cogswell Drain No. 11, and relate wetland habitat loss to observed disease-related mortality among staging waterfowl in fall 1990 and spring 1991. Water regimes of BBMK were exceptionally stable, with few records of drawdowns before 1984 when the clean-out began. After the clean-out (1987-90), BBM were dry by mid-summer in all years and open area declined by 96% by 1990, whereas Kraft Slough (a control area) had water throughout all years and percent open area did not change. Numerous species of waterbirds nested in BBMK before the clean-out, and mean ranks of waterbird density were similar. After the clean-out, waterbirds failed to breed successfully in all years at BBM, and use as major waterfowl staging areas and for waterfowl hunting also ended. At Kraft Slough, use by breeding and staging waterbirds continued in all years, as did waterfowl hunting. Reduced access to fresh water after the Drain No. 11 clean-out may have contributed to a dieoff of 487 lesser snow geese (Chen caerulescens) from necrotic enteritis in Kraft Slough in November 1990. Loss of three major staging areas in Sargent County as a result of the drain clean-out has further concentrated migrant waterfowl, particularly during drought periods, increasing the magnitude of risk when epizootics occur in southeastern North Dakota. Ducks and geese banded in Sargent County have been recovered from 34 and 14 states, 7 and 6 provinces of Canada, and 13 and 1 other countries, respectively, indicating waterfowl populations from a wide area are potentially vulnerable to epizootics when crowded into limited roosting habitat. Despite causing the loss of wetland habitat for thousands of midcontinent waterfowl and other waterbirds, a Federal Court in North Dakota ruled that the clean-out of Drain No. 11 met the criteria necessary to be considered maintenance under Section 404 clause (f)(1)(c) and was not recaptured under clause (f)(2). This outcome suggests current law does not protect wetland functions needed to support migratory waterbird populations or associated recreational values when sites have become naturally restored through lack of maintenance of legal drains.