Zinc (Zn) isotope compositions in soft mussel tissues help identify internal biological processes and track coastal Zn sources in coastal environments, thus aiding in managing marine metal pollution. This study investigated the seasonal and multi-decadal Zn isotope compositions of blue mussels (genus Mytilus) from two French coastal sites with contrasting Zn environmental contamination. Concurrently, we characterized the isotope ratios of sediments and plankton samples at each site to understand the associations between organisms and abiotic compartments. Our primary objective was to determine whether these isotope compositions trace long-term anthropogenic emission patterns or if they reflect short-term biological processes. The multi-decadal isotope profiles of mussels in the Loire Estuary and Toulon Bay showed no isotope variations, implying the enduring stability of the relative contributions of natural and anthropogenic Zn sources over time. At seasonal scales, Zn isotope ratios were also constant; hence, isotope effects related to spawning and body growth were not discernible. The multi-compartmental analysis between the sites revealed that Toulon Bay exhibits a remarkably lower Zn isotope ratio across all studied matrices, suggesting the upward transfer of anthropogenic Zn in the food web. In contrast, the Zn isotope variability observed for sediments and organisms from the Loire Estuary fell within the natural baseline of this element. In both sites, adsorptive geogenic material carrying significant amounts of Zn masks the biological isotope signature of plankton, making it difficult to determine whether the Zn isotope ratio in mussels solely reflects the planktonic diet or if it is further modified by biological homeostasis. In summary, Zn isotope ratios in mussels offer promising avenues for delineating source-specific isotope signatures, contingent upon a comprehensive understanding of the isotope fractionation processes associated with the trophic transfer of this element through the plankton.