A confluence of subarctic, tropical, and subtropical water masses feed the California Current System (CCS), supporting a highly productive ecosystem and wide array of marine ecosystem services. Long-term declines in oxygen have been observed in this region, causing habitat compression and other ecosystem consequences. Here we quantify the water masses and processes causing deoxygenation in the subsurface CCS from 19932018, and we find that deoxygenation was caused both by changes in the advection of source waters and increased remineralization in the source waters. The historical deoxygenation trend can be attributed primarily (81%) to the Northern Equatorial Pacific Intermediate Water, the deep Pacific Equatorial Water mass transported in the California Undercurrent. We also find that advection and remineralization share nearly equal contributions to deoxygenation. This improved understanding of the mechanisms affecting the aerobic habitat of the CCS will inform projections of ecological impacts and mitigation of future deoxygenation.