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