Protected areas in fishery management have been suggested to hedge management failures and variation in harvests. In this paper, a stochastic bioeconomic model of a two-species fishery in the Manning Bioregion is used to test the performance of protected areas as a management tool in a fishery. The establishment of a protected area is analysed under the assumption of heterogenous environments that are linked via density-dependent or sink-source stock dispersal relationships. The sensitivity of the results to different degrees of management is also explored. The model is applied to the Ocean Prawn Trawl, and Ocean Trap and Line fisheries within Manning Bioregion in New South Wales, Australia. The focus of the study is placed on the biological and institutional characteristics that yield benefits to the fishery. It was found that protected area use in the Manning Bioregion is likely to have differing effects on the two fisheries examined, benefiting Ocean Trap and Line fishers but adversely affecting Ocean Prawn Trawl fishers. Overall, it is unlikely that protected area use will lead to an increase resource rent in the fishery.