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Mercury and selenium concentrations and Se:Hg molar ratio in edible muscle and hepatopancreas of the crab Callinectes arcuatus from coastal lagoons of northwest Mexico were determined using atomic absorption spectrophotometry. The three coastal lagoons were Santa Maria La Reforma (SMLR), Urias (UR), and Huizache-Caimanero (HC); samplings were carried out from December 2016 to October 2017. The mercury ranges in the muscle of C. arcuatus in SMLR, UR, and HC lagoons were 0.31–0.52, 0.15–0.45, and 0.22–0.55 μg g−1, respectively. In hepatopancreas, the values ranged from 0.08 to 0.15, 0.06 to 0.15, and 0.05 to 0.12 μg g−1 in SMLR, UR, and HC lagoons, in that order. For selenium concentrations in C. arcuatus muscle, the ranges 11.64–20.14, 14.88–19.71, and 15.27–29.51 μg g−1 were determined in SMLR, UR, and HC lagoons, respectively. While for hepatopancreas, the ranges were 34.34–44.13, 27.77–40.45, and 15.16–49.80 μg g−1, in that order. No significant relationships (p > 0.05) between mercury and selenium concentrations (in white meat and hepatopancreas) were observed in C. arcuatus carapace width and length. Se:Hg molar ratio values were 98.1 ± 20.8, 171.4 ± 81.6, and 176.8 ± 51.2 for SMLR, UR, and HC lagoons, in that order. This high ratio (> 1) in C. arcuatus edible muscle indicated that selenium concentration was sufficient to neutralize possible mercury toxicity, so it does not represent danger to humans when it is consumed.