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Abstract. During the past 20 years, hypoxic areas have expanded rapidly in theBaltic Sea, which has become one of the largest marine “dead zones” in theworld. At the same time, the most important commercial fish population ofthe region, the eastern Baltic cod, has experienced a drastic reduction inmean body condition, but the processes behind the relation betweendeoxygenation and condition remain elusive. Here we use extensive long-termmonitoring data on cod biology and distribution as well as on hydrologicalvariations to investigate the processes that relate deoxygenation and codcondition during the autumn season. Our results show that the depthdistribution of cod has increased during the past 4 decades at the sametime of the expansion, and shallowing, of waters with oxygen concentrationsdetrimental to cod performance. This has resulted in a progressivelyincreasing spatial overlap between the cod population and low-oxygenatedwaters after the mid-1990s. This spatial overlap and the actual oxygenconcentration experienced by cod therein statistically explained a largeproportion of the changes in cod condition over the years. These resultscomplement previous analyses on fish otolith microchemistry that alsorevealed that since the mid-1990s, cod individuals with low condition wereexposed to low-oxygen waters during their life. This study helps to shedlight on the processes that have led to a decline of the eastern Baltic codbody condition, which can aid the management of this population currently indistress. Further studies should focus on understanding why the codpopulation has moved to deeper waters in autumn and on analyzing the overlapwith low-oxygen waters in other seasons to quantify the potential effects ofthe variations in physical properties on cod biology throughout the year.