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The potential for structural changes in time trend concentrations of mercury (Hg), lead (Pb), cadmium (Cd), zinc (Zn), and copper (Cu) in the Mediterranean mussel, Mytilus galloprovincialis, was examined in Mussel Watch (MW) databases of metal pollution at eighteen coastal stations over a decadal period, from 1992 to 2007. Simultaneously, by using two statistical methods representing both the classical hypothesis-testing and the Bayesian approaches, we found single and multiple trend breaks for Hg (28% of the stations), Cd (17%), and Pb (11%) within trends in connection with anthropogenic and subtle natural environmental changes. Also called change point problems, if not accounted for, these could bias time trend investigations and interpretations. We calculated trend rate differences of 39% and switches up to 1 order of magnitude from classical linear trend assessments. We discuss sampling, analytical, and environmental (both natural and anthropogenic) sources of data set variabilities, showing that, in practice, the overall 16-year analytical performance could be as elevated as the yearly sampling reproducibility. We demonstrate that environmental time trend interpretations benefit from undertaking prior structural change analysis. After decades of MW marine chemical pollution assessments these have proven extremely useful, although the occurrence of trend breaks directly affects the long-term marine environmental monitoring strategies. Our results suggest a broader concept to design monitoring programs in agreement with rapid global anthropogenic and environmental changes.