Sea urchin species are ecologically important in the Gulf of California and are becoming popular as a local fishery due their commercial value. The most abundant species are Echinometra vanbrunti, Eucidaris thouarsii, and Tripneustes depressus. The aim of this study was to evaluated cadmium, lead, copper, zinc, and iron concentrations as well as stable isotope values in these sea urchin species in mining area of Santa Rosalia (STR). Metal concentrations were analyzed by atomic absorption spectrophotometry and stable nitrogen and carbon isotopes were estimated using mass spectrophotometry. Highest values of Fe (108.8 mg Kg−1), was found in E. vanbrunti, while highest values of Pb (15.4 mg Kg−1), Cu (14.5 mg Kg−1), and Zn (347.7 mg Kg−1) were found in E. thouarsii; and highest values of Cd (10.8 mg Kg−1) was found in T. depressus. The main ecological risk of trace metal pollution in STR may be caused by Cd and Pb. d15N values were higher in E. thouarsii and d13C in T. depressus, and E. thouarsii have the highest trophic position. There is not relationship between size and metal concentrations, but a positive relation exists between size and isotopic values in T. depressus. The three species showed different bioaccumulation pattern for the metals analyzed. Additionally, collection site and season play an important role in the metal concentration variability. Given that these species are consumed by humans, some risk of trace metals toxicity could be expected due to the accumulation patterns and characteristics of the sites studied.