Organochlorine pesticides (OCP) are legacy anthropogenic compounds known to persist for several years in the environment. The continuous use of some OCP, such as DDT, after restrictions in developing countries are cause of concern, due to their deleterious effects to marine life and humans. Studies assessing OCP contamination in coastal environments are still scarce in South America and there is a need to understand the impacts from trophic chain accumulation of these pollutants in marine life. In this study, we have assessed OCP levels in muscle and liver and estimated the biomagnification factor in several upwelling system trophic chain members, including fish, squid, and marine mammal from Southeastern Brazil. DDT degradation product DDE was the OCP detected in the highest concentrations in Franciscana dolphins (Pontoporia blainvillei), 86.4 ng·g−1 wet weight, and fish muscle and liver. In general, higher OCP levels were found in liver than in muscle, except for croaker. Biomagnification factors (BMF) of OCP in the top predator P. blainvillei and the carnivorous cutlass fish (Trichiurus lepturus) were on average between 0.2 and 1.8. Continued OCP monitoring in this region is warranted to better understand the distribution and fate of these compounds over time, with the goal to establish strategies for the conservation of local dolphin species and to assess human health risks from local coastal region populations.