The Baltic Sea is characterised by a heterogeneous oceanographic environment. The deep water layers forming the habitat of Baltic cod (Gadus morhua callarias L.) are subjected to frequently occurring pronounced anoxic conditions. Adverse oxygen conditions result in physiological stress for organisms living under these conditions. For cod e.g. a direct relationship between oxygen availability and food intake with a decreasing ingestion rate at hypoxia could be revealed. In the present study, the effects of oxygen deficiency on consumption rates were investigated and how these translate to stock size estimates in multi-species models. Based on results from laboratory experiments, a model was fitted to evacuation rates at different oxygen levels and integrated into the existing consumption model for Baltic cod. Individual mean oxygen corrected consumption rates were 0.1–10.9% lower than the uncorrected ones. At the currently low predator stock size, however, the effect of oxygen-reduced consumption on the total amount of eaten prey biomass and thus predation mortalities was only marginal. But should successful management lead to higher cod stock sizes in the future, then total predation mortalities will greatly increase and thus improved precision of these estimates would be valuable for the assessment of prey stocks.