Climate change is warming, deoxygenating, and acidifying the ocean at an unprecedented rate. However, responses to large-scale forcing are variable at relatively small spatial scales, creating marine microclimates. Marine microclimates can provide spatial refuges (safe spaces) or local adaptation that may be harnessed to improve marine conservation and management. We analyze multiyear data sets within two fishing cooperatives in Baja California, Mexico, to quantify small-scale ocean variability, describe the degree to which this variability affects the abundance of species, and discuss the potential for marine microclimates to improve conservation and management efforts. We find that variation in ocean conditions and species abundances at scales of a few kilometers is striking and robust to large-scale climate forcing. We posit that incorporation of marine microclimates into fisheries management and conservation efforts can improve ecosystem sustainability by allowing local adaptation and maintenance of spatial refuges in the face of climate change.