Identifying environmental metrics specific to lesser scaup (Aythya affinis; scaup) spring migration chronology may help inform development of conservation, management and population monitoring. Our objective was to determine how environmental conditions influence spring migration of lesser scaup to assess the effectiveness of the Waterfowl Breeding Population and Habitat Survey in accurately estimating scaup populations. We first compared peak timing of mallard (Anas platyrhynchos) and scaup migration from weekly ground surveys in North Dakota, USA because the Waterfowl Breeding Population and Habitat Survey is designed to capture annual mallard migration. As predicted, we detected that peak timing of scaup and mallard migrations differed in 25 of 36 years investigated (1980–2010). We marked scaup with satellite transmitters (n = 78; 7,403 locations) at Long Point, Lake Erie, Ontario, Canada; Pool 19 of the Mississippi River, Iowa and Illinois, USA; and Presque Isle Bay, Lake Erie, Pennsylvania, USA. We tested the assumption that our marked scaup were representative of the continental population using the traditional survey area by comparing timing of migration of marked birds and scaup counted in the North Dakota Game and Fish Department survey. We detected a strong positive correlation between marked scaup and the survey data, which indicated that marked scaup were representative of the population. We subsequently used our validated sample of marked scaup to investigate the effects of annual variation in temperature, precipitation, and ice cover on spring migration chronology in the traditional and eastern survey areas of the Waterfowl Breeding Population and Habitat Survey, 2005–2010. We evaluated competing environmental models to explain variation in timing and rate of scaup migration at large-scale and local levels. Spring migration of scaup occurred earlier and faster during springs with warmer temperatures and greater precipitation, variables known to influence energy budgets and wetland availability. Our results suggest that surveys designed to index abundance of breeding mallards is imprecise for estimating scaup abundance, and inaccurate at estimating breeding population size by survey stratum.