We developed a geochemical atlas of the Colorado River in Grand Canyon and in its tributary, the Little Colorado River, and used it to identify provenance and habitat use by Federally Endangered humpback chub, Gila cypha. Carbon stable isotope ratios (δ13C) discriminate best between the two rivers, but fine scale analysis in otoliths requires rare, expensive instrumentation. We therefore correlated other tracers (SrSr, Ba, and Se in ratio to Ca) to δ13C that are easier to quantify in otoliths with other microchemical techniques. Although the Little Colorado River’s water chemistry varies with major storm events, at base flow or near base flow (conditions occurring 84% of the time in our study) its chemistry differs sufficiently from the mainstem to discriminate one from the other. Additionally, when fish egress from the natal Little Colorado River to the mainstem, they encounter cold water which causes the otolith daily growth increments to decrease in size markedly. Combining otolith growth increment analysis and microchemistry permitted estimation of size and age at first egress; size at first birthday was also estimated. Emigrants < 1 year old averaged 51.2 ± 4.4 (SE) days and 35.5 ± 3.6 mm at egress; older fish that had recruited to the population averaged 100 ± 7.8 days old and 51.0 ± 2.2 mm at egress, suggesting that larger, older emigrants recruit better. Back-calculated size at age 1 was unimodal and large (78.2 ± 3.3 mm) in Little Colorado caught fish but was bimodally distributed in Colorado mainstem caught fish (49.9 ± 3.6 and 79 ± 4.9 mm) suggesting that humpback chub can also rear in the mainstem. The study demonstrates the coupled usage of the two rivers by this fish and highlights the need to consider both rivers when making management decisions for humpback chub recovery.