Marine reserves are gaining attention around the world as a tool to both conserve ocean resources and improve the productivity of fisheries. Using simulation analysis, we investigate in a limited-entry fishery comprising nine subpopulations the inherent bioeconomic trade-offs associated with cost-effective designs of marine reserve networks' that is, the trade-offs between the degree of connectedness of a site and the biological and economic heterogeneity. We find in many cases that closing two low-value patches can result in larger biological gains and lower costs than closing one high-value patch. We also simulate biological productivity effects after creation of a reserve and find that under special conditions, aggregate sustainable rents are maximized with the closing of a portion of the fishable habitat. Finally, we find that the biological gains of implementing a more rationalized management system can outweigh the gains from closing multiple subpopulations under open access.