Coastal areas are affected by urban, industrial and agriculture pollutants runoff, wastewater and stormwater discharges, making this environment the final repository of chemical contaminants. These contaminants have the potential to spread out to the entire food chain, impacting marine life and the quality of their habitat. In this aspect, the concept of marine mammals as bioindicators provides an approach to the degree of contamination in the environment and to the identification and management of multiple sources of contaminants. The present study analyzed several elements like As, Ba, Cd, Cr, Cu, Hg, Mn, Mo, Ni, Pb, V and Zn in liver tissue from two dolphin species: Sotalia guianensis, a near-threatened species, and the vulnerable Pontoporia blainvillei. In the study, we also investigated if dolphins (population) recorded using the heaviest urban areas have higher concentrations of contaminants in their tissues. Dolphin samples (n = 40 S. guianensis; n = 97 P. blainvillei) were collected by daily monitoring carried out by Santos Basin Beach Monitoring Project (PMP-BS), from stranded individuals found in São Paulo state. The Spearman's rank correlation showed distinct correlations in the accumulation of trace elements by both species, indicating different sources of exposure to the elements studied or distinct biochemical processes between species. Interspecific and intraspecific variations were observed, possibly related to the individual distribution and feeding habits. Correlations were observed between age and concentrations of trace elements, positive for Cd, Hg and Mo. Finally, our findings indicate high levels of Cu, Zn, and concentrations of As, V and Hg in fetuses, in particular, an analysis was performed on a fetus found inside a stranded individual, indicating placental transfer as the first route of exposure for some elements.