Changing ocean conditions are leading to spatial redistribution of many marine species, including those that support fisheries. A combination of gradual climate trends and shorter-lived extreme events, such as marine heatwaves, can change the availability of species or stocks to fishing ports, impacting fishing communities and challenging fisheries management frameworks. Pacific sardine (Sardinops sagax) in the California Current System are currently considered as two subpopulations for management purposes. They are separated from each other using oceanographic conditions, based on the assumption that each subpopulation is associated with different habitats and geographic areas. However, as climate change and marine heatwaves lead to increasingly novel environmental conditions in the region, habitat-based assignments may become impractical or unrealistic. In this study, we use generalized additive models to define sea surface temperature and surface chlorophyll conditions associated with the occurrence of multiple sardine life stages in fishery-independent surveys conducted in the California Current System. We then show how the spatial distribution of habitats across life stages and putative subpopulations may be influenced by both gradual climate change and marine heatwaves. Our results highlight the potential impacts of changing ocean conditions near major sardine landing ports. During recent marine heatwaves, habitat associated with the northern subpopulation became less available to southern California Current ports, and this trend is projected to continue through the end of the 21st century. Future spatial shifts in sardine habitat may increasingly challenge the practicality of habitat-based subpopulation separation and introduce more uncertainty into management frameworks.