Oysters (Ostreidae) play a pivotal role in the health and productivity of marine ecosystems. Their unique ability to filter water, provide habitat, and contribute to nutrient cycling has remained underused in many parts of Europe following the destruction of vast oyster beds in the 19th and 20th centuries. The burgeoning field of oyster restoration for aquaculture has recognized the potential of these bivalves in promoting ecosystem resilience and enhancing biodiversity. Restoring oysters to previous levels requires the establishment of ecological baselines that ideally take into account the long-term changes of animal behavior as well as the surrounding environment prior to significant human intervention, an extremely challenging task. Archaeological shell middens are invaluable baseline archives and provide exclusive insights into past ecosystems. Here, we use demographic information from over 2,000 analyzed European oyster (Ostrea edulis) shells dating from ~5,660 to 2,600 cal BCE (calibrated years BCE), the largest archaeological growth rate dataset of mollusks yet. Through the analysis of size as well as ontogenetic age, we decouple anthropogenic from environmental impacts throughout Denmark. Our data show definitive influence of oyster size-age structure through human harvesting during the Mid-Holocene, with older oysters in the Mesolithic (mean: 4.9 y) than the Neolithic (mean: 3.7 y), irrespective of changes in growth rate. Furthermore, we present the metrics for long-term sustainable harvesting of oysters across environmental and socioeconomic transitions, providing demographic targets for current oyster restoration projects and valuable context in mitigating the impact of modern climatic change.