This study evaluates the effectiveness of Ucides cordatus as a sentinel organism by linking histological and genotoxic biomarkers to environmental contamination, assessed through chemical analyses of water and sediment in two estuarine bays on the Amazon coast of Brazil. Crabs were collected from São José Bay (A1 – minimally impacted) and São Marcos Bay (A2 – impacted by port activities), both in Maranhão State. Concurrently, physicochemical parameters and trace element levels in water and sediment were measured. Biometric data included cephalothorax and cheliped dimensions, movable finger measurements, and total weight. For histological and genotoxic analyses, 20 crabs per site were sampled during both rainy and dry seasons (n=40). Abiotic parameters (pH, dissolved oxygen, salinity) were similar between sites. However, trace element concentrations (Zn, Fe, Al, Mn) in water were higher in A2. Crabs from A2 were significantly smaller and lighter (p < 0.05). Gill lesions, such as marginal canal deformation, pillar cell rupture, and necrosis, were observed at both sites, with greater prevalence in A2. Hepatopancreas alterations, particularly necrosis, were also significantly more frequent in A2 (p < 0.05). Genotoxic biomarkers, including pyknotic nuclei, followed the same pattern, with higher occurrence in A2 (p < 0.05). These findings demonstrate that U. cordatus effectively reflects environmental contamination through measurable histological and genotoxic responses, consistent with chemical evidence of trace element pollution. Elevated trace element levels, reduced biometric parameters, and increased tissue damage in crabs from the impacted site confirm the species’ suitability as a sentinel organism. The integration of biomarker responses with environmental chemistry proved effective in distinguishing contamination levels between sites, supporting its application in environmental monitoring of Amazonian estuaries.