Small-scale fisheries are the ocean’s biggest employers and provide protein and micronutrients to billions, but they are threatened by mounting overfishing. The most prominent and intensely studied strategy to manage near-shore fisheries spatially has been to implement permanent bans on fishing in marine protected areas, yet in many cases these closures fail due to lack of fisher compliance. Temporary closures, on the other hand, are often preferred by fishers around the world to rebuild their fisheries, yet they remain relatively understudied. As a result, there is little understanding of feedbacks and interrelations between the ecological dynamics and effects of these closures and their governance trajectories. Here we propose to bring cutting-edge techniques together in an integrated social, ecological, and modeling research program centered on two research sites where temporary closures have been implemented. Fisher creel surveys, collaborative underwater fish censuses combined with water-based drone habitat monitoring surveys will be employed to provide comprehensive data on the state of the benthos and the fish populations within and outside of the reserves. This will be combined with social science fieldwork focusing on the histories of the reserves, the heterogeneity of stakeholders, local knowledge, and the configurations of property rights that shape stakeholders’ interpretations of a reserve’s socio-ecological outcomes. Drawing from these social and ecological data, dynamic agent-based and bioeconomic models will be adapted from other contexts to generate testable predictions of how temporary closure design affects fish biomass and fisher incomes in the short- and long-term. The outcomes of this research will be used to adapt a decision-tool model to help fishers design temporary closures and it will be tested in several pilot communities.