One of the main obstacles to resolving the conflict between an increasing population of cormorants, Phalacrocorax carbo sinensis, and the fishing industry is the lack of documentation of the effect of the birds’ predation on fish stocks. Tagging and releasing fish with coded wire tags followed by intensive cormorant pellet sampling may be a viable method to measure the impact of cormorants on fish populations. To test this new method, we studied cormorant predation in a shallow estuary, where nearly 100 000 fish were tagged and more than 10 000 cormorant pellets were collected over a 3-year study period. A total of 112 tags were recovered from the collected pellets. Analyses of tag recovery data indicated considerable cormorant predation on tagged flounder, eel and salmon smolts, but the method did not deliver high-quality documentation, mainly because of limitations in pellet sampling. We conclude with recommendations to enhance the value of this method.