Monthly aerial bird counts showed a strong increase in the number of wintering Great Cormorants Phalacrocorax carbo sinensis since the late 1990s at Lake IJsselmeer but not at Lake Markermeer-IJmeer. Compared to the 1980–1990s, breeding numbers also increased in this part of the system. The resulting increased exploitation of fish stocks was thought to have been possible because of a long-term increase in the stock of Ruffe Gymnocephalus cernuus, despite a clear overall decline of total estimated fish biomass in the lake during the same period. The most likely cause of these shifts was thought to be the intensive commercial fishing regime, removing the large predatory fish first, followed by a strong reduction of stocks of large Bream Abramis brama, in turn paving the way for increases in the stocks of Ruffe. Increased predation by Cormorants on the enhanced stocks of small fishes was possible because of ameliorated underwater visibility in Lake IJsselmeer. Starting in 2000, there was a strong shift in both temporal habitat use and associated fish consumption by Cormorants towards the winter period. The local breeding birds, exploiting the same age- and size-structured community of fishes in the spring, thus face an already-depleted food resource. Compared to the 1980–1990s, fish consumption by Cormorants in winter increased by a factor of ten, whereas that by breeders did so by a factor of 1.6. Our calculations showed that the actual harvest of available fish stock by wintering and breeding Cormorants together was c. 5% in 1985–2000 and c. 15% in 2001–2015. The disproportionate division of the overall consumption (‘harvest’) of the fish stock towards the wintering birds is a strong argument for direct competition with their conspecifics breeding locally. In conclusion, we calculate that because of the increased winter exploitation initiated by the activities of an intensive commercial fishery, the fish consumption in summer and early autumn by breeding Cormorants and their offspring was suppressed by a factor of six.