This study was carried out to assess the impacts of heavy metals coming into the Parnaíba River Delta in the Brazilian Northeastern region. The sediment concentrations of different heavy metals, such as Pb, Ni, Cr, Cd, Zn, Cu, Fe, Al and Mn, were measured by flame spectrometry. The sediments were collected from 19 sites distributed along 5 estuarine channels. The average concentrations found for Cu and Zn are compatible with the TEL (Threshold Effect Level). However, Cd concentrations were above the PEL (Probable Effect Level) values, while Ni and Cr showed intermediate mean concentrations. There are no established concentration limits for Mn, Al and Fe. These are the first metal biogeochemistry findings in the area and will contribute to the decision-making of environmental authorities, aiming to control the emissions of metallic pollutants in this important area of the Brazilian coast.