The region of Pontal da Barra is cited by the Tropical Database (BDT) as a priority area for preservation. In this context, we developed a study aimed at determining the levels of heavy metals such as Cu, Pb, Zn in the sediment of this region, the estuary of Patos Lagoon, located in the São Gonçalo Canal that connects with the Lagoon. The sampling took place in May 2010, on seven points. Samples were extracted by acid (3:1 HCl:HNO₃ and 1mL of HClO₄) at 90 °C and the extracts analyzed by flame atomic absorption spectrophotometry. The heavy metal concentrations varied among points: Cu – 4.4 to 13.2mg kg^-1; Pb – 11.67 to 23.21mg kg^-1; Zn of 20.3 to 84.0mg kg^-1. The results show low levels of contamination in comparison with the Canadian Quality Guide for Estuarine Sediments.