Works of art are testimonies to past civilizations and biodiversity, and provide fundamental information for guiding current conservation programs. The success of such programs requires an understanding of the reference state of ecosystems, which is rarely known because current references are in perpetual slippage toward the acceptance of degraded states. For this reason, international organizations are regularly alerted to the fact that fish and aquatic resources are threatened, signaling a major challenge for our societies. In this article we aim to enrich the historical and ecological knowledge of aquatic resources in Western Europe (Atlantic, North Sea, and Mediterranean Sea) by analyzing the taxonomic composition of aquatic biodiversity as represented in Early Modern paintings, using the statistical tools of numerical ecology. The geographic and temporal variations of the biodiversity represented in these paintings are interpreted according to environmental and human pressures, which we differentiate between using technical and socio-cultural "sieves." Our results highlight the natural and anthropic factors that shape the spatial and temporal variations of the aquatic species depicted. These species belong to significantly different periods and regions, with a convergence between the origin of the paintings and the biogeographic area of the species. We show an overall decrease over time of represented taxa, and particularly of continental and freshwater species. We discuss the results in the light of previous works of historical ecology, archeology, history, and biology. Finally, we discuss the relevance and potential future contributions of the method developed herein to better understand the past reference state of aquatic socio-ecosystems.