Cetaceans have been naturally exposed to toxic trace elements (TEs) on an evolutionary time scale. Hence, they have developed mechanisms to control and/or mitigate their toxic effects. These long-lived species located at high trophic positions and bioaccumulating toxic elements are assumed to be good biomonitoring organisms. However, anthropogenic emissions have strongly increased environmental levels of toxic TEs in the last decades, questioning the efficiency of the detoxication mechanisms in cetaceans. In this context, temporal trends of mercury (Hg), cadmium (Cd) and lead (Pb) concentrations were studied through the analysis of 264 individuals from two cetacean species the common dolphin (Delphinus delphis) and the harbour porpoise (Phocoena phocoena) and belonging to two different Management Units (MUs) for the latter. These individuals stranded along the French Atlantic coasts from 2000s to 2017. All the trends presented were age- and sex-corrected and stable isotope ratios of carbon (δ13C) and nitrogen (δ15N) were measured as proxies of their feeding ecology. Results showed that Pb concentrations clearly decreased over time in both species and MUs. This decrease agrees with the lead petrol regulation after 2000s, supporting the use of these species as valuable bioindicators of changes for TE levels in the marine environment. A significant long-term increase of total Hg concentrations was only observed in common dolphins. Cadmium concentrations also revealed different trends over the period in both species. The different Hg and Cd trends observed in the two species, probably reflected a contrasted contamination of habitat and prey species than a global increase of the contamination in the environment. These results highlight the necessity and gain of using different species to monitor changes in marine environments, each of them informing on the contamination of its own ecological niche. Lastly, the Se:Hg molar ratios of species suggested a low risk for Hg toxicity over time.