Given the importance of coastal upwelling systems to ocean productivity, fisheries, and biogeochemical cycles, their response to climate change is of great interest. However, there is no consensus on future productivity changes in these systems, which may be controlled by multiple drivers including wind‐driven and geostrophic transport, stratification, and source water properties. Here we use an ensemble of regional ocean projections and recently developed upwelling indices for the California Current System to disentangle these sometimes‐competing influences. Some changes are consistent among models (e.g., decreased mixed layer depth), while for others there is a lack of agreement even on the direction of future change (e.g., nitrate concentration in upwelled waters). Despite models' diverging projections of productivity changes, they agree that those changes are predominantly driven by subsurface nitrate concentrations, not by upwelling strength. Our results highlight the need for more attention to processes governing subsurface nutrient changes, not just upwelling strength. Plain Language Summary The California Current System is one of the world's eastern boundary upwelling systems—some of the most productive regions in the global ocean. These regions support a wide range of human activities, such as fisheries and tourism, motivating extensive research on how they might evolve under future climate change. A number of hypotheses have been offered to describe future physical and chemical change in these systems, and in terms of their impacts on primary production (which forms the base of the marine food web), these mechanisms may reinforce or oppose each other. Enhanced nutrient concentrations in upwelling source waters would support higher productivity, increased stratification would limit nutrient supply and productivity, and increased upwelling could enhance productivity to a point but limit productivity if it is too strong. There is no consensus on which mechanism(s) will predominantly drive future productivity changes. Here we provide a detailed analysis of projected physical and biogeochemical changes and how they relate to productivity changes. Even though different models project different futures, we find that in all of them the primary control on productivity is the nitrate concentration of subsurface waters, not the strength of upwelling, which has received more attention to date. Key Points Future changes in the California Current System are evaluated using an ensemble of downscaled ocean projections We evaluate changes in Ekman and geostrophic transports, water column structure, and subsurface nitrate concentrations Across models, phytoplankton biomass changes are more closely tied to subsurface nitrate concentration than upwelling strength