Bioaccumulation patterns of heavy metals (Pb, Cd, Cr, Ni, Fe and Cu) and organic (priority and emerging) pollutants, in combination with stable isotope analysis (SIA), were assessed in muscle and liver of three tuna species from the Gulf of Cadiz (Atlantic bluefin tuna, Thunnus thynnus; Atlantic bonito, Sarda sarda, and skipjack tuna, Katsuwonus pelamis). SIA and contaminant (heavy metal and organic) profiles separately discriminated between species. There was no significant overlap between the trophic niches estimated from isotopic data, suggesting that there are diet differences which may determine differential bioaccumulation patterns. The levels of heavy metals and persistent organic pollutants in muscle of all the individuals analyzed were below the allowable limits established by the current legislation. Concentrations of most contaminants were higher in liver than in muscle, underlining the powerful detoxifying capacity of the liver in tunas. In addition to diet, other factors such as size and age (exposure time to environmental chemicals) explain differences in pollutant accumulation patterns in tissues between species, each with varying degrees of involvement depending on the pollutant class. Our results show that combining contaminant profile data with trophic features based on SIA may help understand pollutant bioaccumulation patterns in upper levels of marine food webs.