I use microchemistry in fish otoliths to test the hypothesis that diverting Colorado River flow from reaching the Gulf of California has impacted two endemic fish: the threatened gulf Corvina, (Cynoscion othonopterus) and the endangered totoaba (Totoaba macdonaldi). The oxygen and carbon stable isotope ratios in otoliths help to reconstruct conditions of the environment during key life history stages before and after the damming and diverting the Colorado River. The δ¹⁸O in otoliths illustrate that both C. othonopterus and T. macdonaldi seek out brackish habitat provided by the Colorado River during their early life history. The δ¹⁸O of C. othonopterus otolith have a strong negative correlation with Colorado River flow. I found that previously published relationships between otolith δ¹⁸O and ambient temperature along with δ¹⁸O of the water are sufficient to predict ranges of expected δ¹⁸O values for T. macdonaldi in the field. The δ¹⁸O in pre-dam T. macdonaldi otoliths show significant divergence from modern T. macdonaldi otoliths’ values, indicating that these fish used the brackish waters of the Colorado River estuary. The δ¹³C in T. macdonaldi otoliths has a significant proportion of its δ¹³C derived from diet. Pre-dam T. macdonaldi juveniles have a significantly different diet, which reflects that the Colorado River estuary had higher productivity before diversion of the river. Lastly, T. macdonaldi grew faster before the dams and in association with Colorado River flow measured by the δ¹⁸O.