Climate change is altering the environmental conditions of aquatic ecosystems worldwide at an unprecedented rate, increasing water temperatures and disrupting chemical regimes. Consequently, species can either adapt or experience reductions in fitness, contractions in their distributional ranges, or even extinction. Recent advances in genomic technologies have made it increasingly feasible to sequence large numbers of individuals at reduced costs and to reliably recover genomic data from modern as well as historical and ancient specimens. By comparing allele frequencies along environmental gradients in both time and space, our research aims to identify the key genomic adaptations that allow species to thrive in distinct climates and environments and predict the consequences of both past and future climate change on different populations of multiple species. Using a combination of published genomic datasets from contemporary populations and newly generated sequences from contemporary and ancient samples sourced through a network of collaborators, we focus on abundant and widely distributed species of high ecological and economic value (e.g. Atlantic herring, lesser Sandlance, Atlantic cod, the red swamp crayfish, Atlantic mackerel, European anchovy). As a first step, we employ a comparative landscape genomics approach to consolidate and expand current knowledge on population structure and genomic variation (both point mutations and structural variants) responsible for local adaptation to the environment. Second, when ancient and historical samples are available, we reconstruct the genetic impacts of past climate fluctuations and human disturbances by establishing pre-disturbance baselines of genetic indicators for comparison and by tracking changes in adaptive genetic variation through time and across space. Finally, we develop individual-based simulations and landscape models to predict how different future climate projections will impact the distribution, connectivity, abundance, and resilience of the studied species. Altogether, our research aims to understand how environmental gradients shape the genetic composition, how species have adapted to historical environmental change, and how future climatic shifts may affect survival and distribution, ultimately impacting ecosystem conservation and management.