The North American Waterfowl Management Plan highlights the importance of enhancing waterfowl habitat for productivity and resilience. Many forms of land management are conducted in wetlands to support the diverse communities of waterfowl and other species. Primary burrowing crayfish are also abundant and important in these environments, but little research is available assessing the effects of waterfowl land management on primary burrowers. We examined the response of the digger crayfish, Creaserinus fodiens, to the common vegetation management practices of mowing and disking at waterfowl conservation areas in south-eastern Missouri. Our results demonstrated that at a fine scale, crayfish density was affected by only canopy cover. We also highlighted distributional effects of landscape-level environmental variables and suggested that habitat generalists were tolerant of vegetation management, responding more to vegetation composition and broader landscape effects. We discuss wetlands conservation practices and suggest that burrowing crayfish management would integrate well with some current management strategies for waterfowl.