The use of marine protected areas as a fishery management tool has been suggested as a hedge against management failures and variation in harvests. If successful, protected areas have the potential to increase the level of resource rent derived from the extraction of fishery resources. In this paper, a stochastic bioeconomic model of a multi-species fishery is used to test the performance of protected areas as a management tool in a two patch, two species fishery with heterogeneous environments. The differences in the environments occur through each patch having its own growth rates and internal dynamics. Protected areas are analyzed under density-dependent and sink-source dispersal relationships between the environments within the fishery. These relationships define the drivers of the dispersal of biomass, and as such, will influence the outcome from protected area creation. The model is applied to a section of the NSW fishing industry located in the Manning Bioregion. The NSW Government has committed to the establishment of a representative system of marine parks in coastal waters. The aim of protected area creation is to protect unique elements of NSW marine habitats. The primary focus for protected area establishment is not as a tool for fisheries management; however, it is likely to lead to some effects on the NSW commercial fishing industry. In 2004, an assessment of the Manning Self Bioregion, which spans north of the Hunter river to north of Nambucca Heads, was completed and identified an area between Stockton Beach and Wallis Lake as the likely area for a new marine park The results from the model under the assumption homogenous catch show that protected area can be used as a fisheries management tool in the Manning Bioregion under certain conditions. Both the nature and extent of the dispersal from the protected area are key features in determining the economic outcome from protected area creation. The greater the level of dispersal, the greater the benefits from protected area establishment as more of the biomass that occurs within the protected area is likely to flow to the surrounding fishery, offsetting the effects of reduced fishing area. The value of small sized protected areas is enhanced through the density-dependent flows. Under sink-source flows, differences in relative densities do not encourage increased flows from the protected areas due to differences in patch population density, making the level of dispersal more dependent on protected area size. Given this, when sink-source flows are likely, a minimum size protected area is required before benefits to the fishery can be obtained. The creation of a marine protected area in the Manning Bioregion is likely to have different distributional effects on the two fisheries examined in this paper. For the prey fishery, the Ocean Prawn Trawl Fishery, the benefits of protected area creation are limited by the effects of predation. As such, the protected area is less likely to increase harvests and fishery rent post establishment. Further, certain sized protected areas increased the variability of harvests, meaning that overall harvests were not only reduced but more variable. The counter occurred for the predator fishery, the Ocean Trap and Line Fishery, which is more likely to benefit from protected area creation as increased prey and the removal of fishing pressure increased the biomass of targeted species in the fishery. Despite the potential gain, in the open fishing grounds harvests of these species is likely to become more variable. For the two fisheries as a whole, the creation certain sized protected areas can yield some hedge benefits in terms of overall harvests and resource rent. However, for this to occur, a minimum size is required. Small sized protected areas are less likely to yield hedge benefits to the fishery, with medium to large more likely. The reason for this is that smaller sized protected areas do not increase biomass greatly above exploited levels, reducing the ability for biomass in the protected area to reduce normal fluctuations in populations caused through environmental stochasticity.