In this study, we analyzed biomarkers and heavy metals in Ucides cordatus specimens caught in mangrove areas [A1 = reference (low impact area); A2, A3 and A4 = port complex (potentially impacted area)] of the Amazonian northern coast of Brazil. Sediments and crab muscles sampled from the potentially impacted mangroves showed high levels of metals. Additionally, catalase and glutathione S-transferase enzymes in the gills and hepatopancreas of the collected crabs were elevated in crabs from A2, A3 and A4 relative to those from A1. The histological characteristics of the gills and hepatopancreas differed in crabs collected from A2, A3 and A4 compared with those collected from A1. The crabs were larger and heavier in the rainy season in A1 and A3 and heavier in the dry season in A4. Heavy metal analyses of sediments, crab muscles and biological responses indicated that the animals are subjected to stress levels differentiated in the mangroves due to a gradient (A4>A3>A2>A1) of anthropogenic pressure in São Marcos Bay. In conclusion, the analyses of metals in the sediment and in the muscles of crabs, as well as the biochemical biomarker and histological analyses, suggest that crabs from mangroves in the port complex region are subject to pollutants that compromise their health.