The use of marine protected areas as a fishery management tool has been suggested as a hedge against management failures and variation in harvests. A stochastic bioeconomic model of a hypothetical predator–prey fishery is used to test the performance of protected areas in a fishery with heterogenous environments. Protected areas are analysed under density-dependent and sink-source dispersal relationships between the subpopulations that occur within the fishery. Differing management structures governing resource extraction are analysed. The focus of the study is placed on the biological and management characteristics that yield benefits to both fishers and society. It is shown that the establishment of a protected area improves fishery rent and lowers harvest variation. This result is sensitive to both current management controls and the correlation between species and patches.