This investigation evaluated the bioaccumulation potential of the tropical estuarine bivalve Anomalocardia flexuosa for trace metals. To this aim, chemical and sedimentological analyses and bioaccumulation tests were performed. The sediments were mainly composed by fine-sands and mud, with variable levels of organic matter and CaCO3. Muddy sediments from a depositional site (P2) presented the highest concentrations of metals, despite SEM/AVS not indicating bioavailability. Bioaccumulation factors showed high ratios for Cd, Ni, and Zn, while associations between the contents of mud, organic matter, CaCO3 and metals in sediments and tissues of A. flexuosa were indicated by a principal component analysis. The SEM/AVS was not effective to predict the bioavailability through dissolved metals. The results showed that contaminants were bioavailable, while the performed bioaccumulation test proved to be a reliable technique for assessing sediment contamination in estuarine regions. Moreover, A. flexuosa was considered an adequate test organism for bioaccumulation studies.