Geochemical methods for distinguishing salmon of different runs would improve management practices designed to mitigate for declines in salmon populations in California's Sacramento–San Joaquin river system. Strontium isotopic measurements show a strong relationship between the 87Sr/86Sr ratio in hatchery water and the 87Sr/86Sr ratio in the otoliths (aragonitic ear bones) of juvenile chinook salmon (Oncorhynchus tshawytscha) raised in those waters. As a result of differences in basin geology from north to south along the western slope of the Sierra Nevada, important salmon spawning rivers within the Sacramento–San Joaquin river system have distinct 87Sr/86Sr ratios. Of the 10 rivers in this study, those in the Sacramento River drainage have lower 87Sr/86Sr ratios (0.7039–0.7063) than those in the San Joaquin River basin (0.7068–0.7092), with the exception of the American River, which has the highest 87Sr/86Sr ratios in this study (average 0.7100). The combination of distinct river 87Sr/86Sr ratios and the relationship between water and otolith Sr isotope ratios indicates that this geochemical method can be used to identify the origin (and potentially the migration history) of juvenile, out-migrating salmon in the Sacramento–San Joaquin system.