Climate change and deoxygenation are affecting fish stocks on a global scale, but disentangling the impacts of these stressors from the effects of overfishing is a challenge. This study was conducted to distinguish between climate change and mismanagement as possible causes for the drastic decline in spawning stock size and reproductive success in cod (Gadus morhua) and herring (Clupea harengus) in the Western Baltic Sea, when compared with the good or satisfactory status and reproductive success of the other commercial species in the area. Available data on water temperature, wind speed, and plankton bloom during the spawning season did not reveal conclusive correlations between years with good and bad reproductive success of cod or herring. Notably, the other commercial species in the area have very similar life history traits suggesting similar resilience against stress caused by climate change or fishing. The study concludes that severe, sustained overfishing plus inappropriate size selectivity of the main fishing gears have caused the decline in spawning stock biomass of cod and herring to levels that are known to have a high probability of impaired reproductive success. It is pointed out that allowed catches were regulated by management and adhered to by the fishers, meaning that unregulated fishing did not occur. Thus, mismanagement (quotas that were too high and gears that selected too small sizes) and not climate change appears to be the primary cause of the bad status of cod and herring in the Western Baltic Sea.