Conservation planning traditionally relies upon static reserves, however there is increasing emphasis on dynamic management (DM) strategies that are flexible in space and time. Due to its novelty, the field of DM lacks best practices to guide design and implementation. We assess the effect of planning unit (PU) size within the context of an applied DM tool designed to reduce entanglements of protected whales in a lucrative U.S. crab fishery. We find that smaller PUs avoided up to $47M of revenue loss and reduced entanglement risk by up to 25% compared to the large PUs currently in use by avoiding the incidental closure of lose-lose areas with low biodiversity value and high fisheries revenue. However, larger PUs were more buffered against the effects of an unprecedented marine heatwave in 2014–16, and were less affected by delays in data availability. Our findings suggest that novel and adaptive management solutions - rather than a one-size-fits-all approach - are needed to separate wildlife from their threats under a changing climate.