The lower Roanoke River in North Carolina, USA, has been regulated by a series of dams since the 1950s. This river and its floodplain have been identified by The Nature Conservancy, the US Fish and Wildlife Service, and the State of North Carolina as critical resources for the conservation of bottomland hardwoods and other riparian and in-stream biota and communities. Upstream dams are causing extended floods in the growing season for bottomland hardwood forests, threatening their survival. A coalition of stakeholders including public agencies and private organizations is cooperating with the dam managers to establish an active adaptive management program to reduce the negative impacts of flow regulation, especially extended growing season inundation, on these conservation targets. We introduce the lower Roanoke River, describe the regulatory context for negotiating towards an active adaptive management program, present our conservation objective for bottomland hardwoods, and describe investigations in which we successfully employed a series of models to develop testable management hypotheses. We propose adaptive management strategies that we believe will enable the bottomland hardwoods to regenerate and support their associated biota and that are reasonable, flexible, and economically sustainable.