Spawning grounds and juvenile habitats are critical essential fish habitats (CEFH) facing multiple anthropogenic pressures. Yet the impacts of these pressures on fish population dynamics are poorly quantified. In this study, we address the impact of hypoxia on CEFH and its consequences on the productivity of exploited marine fish populations. Our approach relies on an age- and stage-structured simulation model, including habitat effects on egg, juvenile, or spawner mortalities to integrate the impact of hypoxia on spawning and juvenile habitats. We applied this framework in the Baltic Sea (BS) to explore population responses of cod, plaice, and herring, which face hypoxic conditions in their CEFH. All scenarios lead to modifications in fishing mortality, population size, and yield at maximum sustainable yield, but with different magnitudes depending on the impacted life stage. Perturbations of spawning habitats that result in higher mortality of eggs had the least impact, while the more direct effect on spawners themselves had the largest impact. Within each scenario, the responses also depended upon species and life history traits, with contrast in steepness and lifespan that explain most of the differences between species. Cumulative impacts of pressures in both CEFH were also investigated and revealed mainly nonadditive responses. Our framework is a generic tool, transferable to a large panel of case studies, to quantify the relative impact of CEFH degradation/restoration for the dynamics of marine exploited populations.