The present work analyzed the concentration of As, Cd, Pb, and Hg in sediment and the Hg concentration in fish muscle from two coastal lagoons in the states of Jalisco (Barra de Navidad Lagoon) and Colima (Cuyutlán Lagoon), Mexico. Both lagoons showed relatively low levels of metal contamination and potential health risk compared to other Mexican areas. A non-carcinogenic hazard quotient (HQ) was determined. As (10.7 ± 1.3 - 25.4 ± 3.1 μg g-1) and Pb (42.7 ± 4.2 - 123.9 ± 14.7 μg g-1) concentrations exceeded the permissible levels, otherwise for Hg and Cd were below the limits. The highest total mercury concentration was found in Haemulopsis sp. and Lutjanus sp. with 0.23 and 0.1 μg g-1 (wet weight) respectively, out of 14 species of fish analyzed that are frequently consumed locally. HQ based on the national daily per capita consumption of fish in Mexico and the consumption of fish associated with fishing communities in Mexico showed an HQs >2, which manifests the vulnerability of these communities to persistent toxic and bioaccumulative contaminants.