No-take marine reserves can be powerful management tools, but only if they are well designed and effectively managed. We review how ecological guidelines for improving marine reserve design can be adapted based on an area’s unique evolutionary, oceanic, and ecological characteristics in the Gulf of California, Mexico. We provide ecological guidelines to maximize benefits for fisheries management, biodiversity conservation and climate change adaptation. These guidelines include: representing 30% of each major habitat (and multiple examples of each) in marine reserves within each of three biogeographic subregions; protecting critical areas in the life cycle of focal species (spawning and nursery areas) and sites with unique biodiversity; and establishing reserves in areas where local threats can be managed effectively. Given that strong, asymmetric oceanic currents reverse direction twice a year, to maximize connectivity on an ecological time scale, reserves should be spaced less than 50–200 km apart depending on the planktonic larval duration of target species; and reserves should be located upstream of fishing sites, taking the reproductive timing of focal species in consideration. Reserves should be established for the long term, preferably permanently, since full recovery of all fisheries species is likely to take > 25 years. Reserve size should be based on movement patterns of focal species, although marine reserves > 10 km long are likely to protect ~ 80% of fish species. Since climate change will affect species’ geographic range, larval duration, growth, reproduction, abundance, and distribution of key recruitment habitats, these guidelines may require further modifications to maintain ecosystem function in the future.