Fall-run Chinook salmon (Oncorhynchus tshawytscha) from the Sacramento-San Joaquin River system form the backbone of California’s salmon fishery and are heavily subsidized through hatchery production. Identifying temporal trends in the relative contribution of hatchery- versus wild-spawned salmon is vital for assessing the status and resiliency of wild salmon populations. Here, we reconstructed the proportion of hatchery fish on natural spawning grounds in the Feather River, a major tributary to the Sacramento River, using strontium isotope (87Sr/86Sr) ratios of otoliths collected during carcass surveys from 2002-2010. Our results show that prior to the 2007-2008 salmon stock collapse 55-67% of in-river spawners were of hatchery origin; however, hatchery contributions increased drastically (89%) in 2010 following the collapse. Data from a recent hatchery marking program corroborate our results, showing that hatchery fish continued to dominate (~90%) in 2011-2012. Though the rebound in abundance of salmon in the Feather River suggests recovery of the stock post-collapse, our otolith chemistry data document a persistent decline of wild spawners, likely leading to the erosion of locally-adapted Feather River salmon populations.