We compared the effectiveness of marine reserve networks designed using a numerical optimization tool with networks designed by stakeholders during the course of California's Marine Life Protection Act Initiative at representing biodiversity and minimizing estimated negative impacts to fishermen. We used the same spatial data representing biodiversity and recreational fishing effort that were used by the stakeholders to design marine reserves. In addition, we used commercial fishing data not explicitly available to the stakeholders. Networks of marine reserves designed with numerical optimization tools represented the same amount of each habitat, or more, and had less of an estimated impact on commercial and recreational fisheries than networks designed by the stakeholders. The networks designed by the stakeholders could have represented 2.0–9.5% more of each habitat with no additional impact on the fisheries. Of four different marine reserve proposals considered in the initiative, the proposal designed by fishermen was more efficient than the proposals designed by other stakeholder groups at representing biodiversity and minimizing impact to the fishing industry. These results highlight the necessity of using comprehensive information on fishing effort to design a reserve network that efficiently minimizes negative socioeconomic impacts. We recommend that numerical optimization tools support, not replace, the stakeholder-driven reserve design process along California's northern and southern coasts to help accomplish two of the initiative's core objectives: (1) Protect representative and unique marine habitats, and (2) Minimize negative socioeconomic impacts. The involvement of stakeholders is necessary as additional factors important to reserve design can not be considered using a numerical optimization tool.