Recent changes in climate and environment, influenced by both global and local factors, have had profound impacts on coastal ecosystem functioning and trajectories. By examining archived samples from ongoing ecological monitoring efforts, particularly focusing on bivalves like mussels and oysters, we gain a valuable long-term perspective on how ecosystems are responding at various scales. We conducted analyses on carbon and nitrogen elemental and isotopic ratios (C:N, δ13C, δ15N) of mussel and oyster soft tissues collected annually at 33 sites along the French coast from 1981 to 2021. This extensive dataset (https://doi.org/10.17882/100583, Liénart et al., 2024a) offers a comprehensive view spanning multiple decades and ecosystems, allowing to track how coastal ecosystems and marine species record changing climate, physical-chemical environments and organic matter cycles. Additionally, these data are crucial for establishing isotope baselines for studying food webs. Ultimately, this data set provide valuable information for more effective ecosystem conservation and management strategies in our rapidly changing world.