During the past 20 years, hypoxic areas have expanded rapidly in the Baltic Sea, which has become one of the largest marine "dead zones" in the world. At the same time, the most important commercial fish population of the region, the eastern Baltic cod, has experienced a drastic reduction in mean body condition, but the processes behind the relation between deoxygenation and condition remain elusive. Here we use extensive long-term monitoring data on cod biology and distribution as well as on hydrological variations to investigate the processes that relate deoxygenation and cod condition during the autumn season. Our results show that the depth distribution of cod has increased during the past 4 decades at the same time of the expansion, and shallowing, of waters with oxygen concentrations detrimental to cod performance. This has resulted in a progressively increasing spatial overlap between the cod population and low-oxygenated waters after the mid-1990s. This spatial overlap and the actual oxygen concentration experienced by cod therein statistically explained a large proportion of the changes in cod condition over the years. These results complement previous analyses on fish otolith microchemistry that also revealed that since the mid-1990s, cod individuals with low condition were exposed to low-oxygen waters during their life. This study helps to shed light on the processes that have led to a decline of the eastern Baltic cod body condition, which can aid the management of this population currently in distress. Further studies should focus on understanding why the cod population has moved to deeper waters in autumn and on analyzing the overlap with low-oxygen waters in other seasons to quantify the potential effects of the variations in physical properties on cod biology throughout the year.