This study investigates future temperature changes in the surface and benthic layers of the North Sea and the Baltic Sea using a high-resolution, three-dimensional regional hydrodynamic ensemble. To simulate future ocean states, we forced our regional ocean model with a five-member atmospheric ensemble from EURO-CORDEX, using their dynamically downscaled variables under the high-emission RCP8.5 pathway across three 30-year climatological time slices: historical (1971–2000), near-future (2031–2060), and far-future (2071–2100). Rigorous validation against long-term satellite observations reveals systematic, seasonally dependent model biases, marked by winter overestimation and summer underestimation of sea surface temperatures (SST). To mitigate these anomalies, a monthly linear scaling (MLS) bias correction scheme is implemented. Projections indicate an accelerated three-dimensional warming trend toward the end of the century, with pronounced regional hotspots exceeding 4–5 °C in semi-enclosed arctic-amplification zones like the Bothnian Bay and the Gulf of Finland. To demonstrate why bias correction is vital and to illustrate the socioeconomic and ecological value of bias-corrected projections, the model results are converted into two sector-specific indicators. The surface-based "bathing suitability index" reveals an expansion of water temperatures above 20 °C along the western Baltic coast, indicating prolonged tourist seasons alongside heightened risks of pathogenic <em>Vibrio</em> proliferation. Moreover, the bottom-based "spawning survival index" suggests that spring sea bottom temperatures (SBT) in the North Sea will consistently transcend the optimal 7 °C threshold for Atlantic cod (<em>Gadus morhua</em>), driving an inevitable northward habitat migration. These results highlight the critical necessity of surface and vertical bias correction when deploying hydrodynamic models to inform regional climate adaptation frameworks.