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Piscivorous birds in aquatic ecosystems exert predation pressure on fish populations. But the site‐specific impact on fish populations, including stocked and commercially used fish species, remains disputed. One of the key questions for the management of piscivorous birds and fish is determining the origin of prey and thus which fish populations are targeted by the birds. We addressed this question by provenancing otoliths (earstones) of fish obtained from regurgitated pellets of piscivorous birds by otolith microchemistry analysis. We retrieved otoliths from regurgitated pellets of great cormorants (Phalacrocorax carbo sinensis) collected every 2 weeks for 2 years from breeding and roosting colonies at Chiemsee in Bavaria, Germany, and classified them according to family or species. We collected water samples from Chiemsee and potential surrounding foraging grounds. We measured the strontium (Sr) 87Sr/86Sr isotope ratio and Sr mass fraction of water and otoliths using (laser ablation) inductively coupled plasma‐mass spectrometry. We assigned otoliths from regurgitated pellets to habitat clusters of origin by comparing the Sr isotopic and elemental composition of otoliths and waterbodies. In 36% of cormorant pellets collected at Chiemsee, prey was assigned to waterbodies distinct from Chiemsee. Furthermore, cormorants used different foraging sites during 1 day. Microchemical provenancing of prey remains can contribute to identifying foraging sites of piscivorous birds and to what extend the birds switched among foraging sites. [ABSTRACT FROM AUTHOR]