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Abstract The Navachiste complex (NAV) is impacted by neighbored human activities and is located in the southwestern coastal zone of the Gulf of California. The study determines the trace metal (TM) and organochlorine pesticides (OCP) health risk content in the edible tissue of Sphoeroides spp. from NAV. The daily intakes (EDI), target hazard quotient (THQ), hazard index (HI), and carcinogenic and non-carcinogenic risks were calculated. Twenty OCP and seven TM were detected. Cd, Cu, Fe, Mn, Pb, and Zn were above MRLs. The γ‒Chlordane was the most frequent OCP. The highest average concentration was for α‒HCH, followed by γ‒chlordane. With the high ratios of γ‒HCH, p, p′‒ DDD and p, p′‒DDD, and the absence of p, p′‒ DDT, the higher ratios for dieldrin and endrin than for aldrin, α‒ chlordane, γ‒chlordane, heptachlor, and heptachlor epoxide indicates historical contamination. In contrast, the residual products of methoxychlor, endosulfan, and its isomers indicate endosulfan's recent use. The TM EDI, THQ > 1 (at 120 g day−1), and the ILCR (> 1 × 10–6) were above minimum levels, showing a high-risk potential for cancer development in the long term.