The decline of the Eastern Baltic cod (Gadus morhua) stock from highest to lowest stock levels on record throughout the 1980s and early 1990s was caused by a combination of recruitment failure and increasing fishing pressure at declining stock sizes. The processes driving the reproductive success are largely understood, but the consequences of these changes for fisheries management are far less evident. This includes doubts about the adequacy of the biological reference points presently used to advise on the stock status, and the need of their revision given that environmental changes have affected stock productivity. Long-term projections suggest that under adverse environmental conditions for reproduction, harvesting at fishing mortality determined as precautionary may not lead to a recovery of the stock to a biomass level considered precautionary. Thus, a revision of either the limit fishing mortality or the limit biomass reference point is indicated. However, an accepted methodology to determine these reference points in situations of changing stock productivity or system carrying capacity does not exist. Environmental conditions affecting recruitment matter not only for the determination of limit reference points, but according to long-term simulations also for target fishing mortalities, being central parts of harvest control rules in several management plans.