Marine protected areas (MPAs) are zones geographically delimited under pre-defined management goals, seeking to reduce anthropogenic threats to biodiversity. Despite this, in recent years reports of MPAs affected by chemical contamination has grown. Therefore, this study addresses this critical issue assessing legacy and current chemical contamination in filter-feeder bivalves obtained in very restrictive no-take MPAs from Brazil. The detected pollutants encompass polycyclic aromatic hydrocarbons (PAHs), linear alkylbenzenes (LABs), and persistent organic pollutants (POPs) like dichlorodiphenyltrichloroethane (DDTs) and polychlorinated biphenyls (PCBs). Despite protective measures, bivalves from nine MPAs exhibited high LABs (13.2–1139.0 ng g−1) and DDTs levels (0.1–62.3 ng g−1). PAHs were present in low concentrations (3.1–29.03 ng g−1), as PCBs (0.7–6.4 ng g−1), hexachlorobenzene (0.1–0.2 ng g−1), and Mirex (0.1–0.3 ng g−1). Regardless of the sentinel species, MPAs and management categories, similar accumulation patterns were observed for LABs, DDTs, PAHs, and PCBs. Based on the limits proposed by Oslo Paris Commission, the measured levels of PAHs, PCBs and were below the environmental assessment criteria. Such findings indicate the no biological effects are expected to occur. However, they are higher considering background conditions typically measured in remote or pristine areas and potential simultaneous exposure. Such findings indicate an influence of anthropogenic sources, emphasizing the urgency for monitoring programs guiding strategic management efforts to safeguard these areas.