The present work tested whether ecological and biological parameters have an influence on the accumulation of trace elements and organic mercury (HgOrg) by the liver and kidney of coastal (Pontoporia blainvillei, N = 31; Sotalia guianensis, N = 21) and oceanic (Stenella coeruleoalba, N = 3; Stenella frontalis, N = 4) cetaceans species incidentally caught in fishing nets along two Brazilian coastal areas (tropical - northern Rio de Janeiro State and subtropical -Rio Grande do Sul State). This research added new insight to the existing studies with trace element concentrations in internal organs of marine cetaceans from the southwestern Atlantic Ocean. Few studies have documented trace element concentrations in marine mammals in this area. Analytical methodologies based on atomic absorption spectrometry (AAS), using the graphite furnace (GF-AAS) and cold vapor (CV-AAS) techniques were applied for this purpose. They are the most popular analytical techniques applied for trace element and mercury determination, respectively, in biological samples. Precision and accuracy of the analytical methods were determined and monitored using certified material from National Research Council - Canada (DORM-2, DOLT-2 and TORT- 2). Interspecies (coastal and oceanic cetacean species) and regional (tropical and subtropical regions) differences were observed in the accumulation of trace elements and organic mercury in organs, liver and kidney. The highest concentrations of these elements were observed in the liver of the oceanic cetacean species. However, no gender differences were found on the bioaccumulation of trace elements and also organic mercury. Biological parameters such as, population, body length and sexual maturity influenced on the trace element and organic mercury accumulation by both organs, according to the cetacean species and caught area. S. guianensis, which co- habits the same coastal marine environment that P. blainvillei species, was the only dolphin species that presented a Se:Hg molar ratio close to 1:1, showing that a probable detoxification process can be occurring in the liver of S. guianensis. This dolphin species feeds mainly on predatory fish, while P. blainvillei feeds mainly on fish and cephalopods. P. blainvillei presented a Se:Hg molar ratio close to 4:1. It`s known that transition metals, such as Hg, Cd and Ag, have an interaction with Se in the liver of marine mammals. The molar concentrations of Cd (p = 0.01) and Ag (p < 0.001) presented significant correlations with the hepatic molar Se in the liver of S. guianensis. P. blainvillei from both sampling areas presented a high significant correlation for molar Se to Hg concentrations (p < 0.001) in liver. Meanwhile, only individuals of P. blainvillei from tropical region showed a significant correlation with hepatic Se and Cd (p < 0.001). Based on the results present here, it is possible to conclude that, not only the different environmental conditions, but also life span, growth stage but mainly the feeding habit influenced the accumulation of trace elements and organic mercury by cetacean tissues. These ecological and biological parameters influenced on the inter-element relationships.