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Capsule A new method of estimating winter Great Cormorant population trends was developed to improve monitoring. Aims To develop methods of estimating Cormorant population trends with confidence intervals by combining data from different monitoring schemes. Methods Estimates of inland and coastal winter Cormorant populations were made for England and Wales from 1988 to 2010. Annual counts from the Wetland Bird Survey were used, supplemented with Dispersed Waterbird Survey data for inland populations, and Non-Estuarine Coastal Waterbird Survey data for coastal populations. Bootstrapping was undertaken to produce confidence intervals. Results The winter Cormorant population in England and Wales increased by about 59% between 1988 and 2010. The annual trend of the inland population became less positive from 2004 onwards, the year in which numbers controlled under licence greatly increased. Conclusions The improved precision of the new estimates provides a sound basis on which to assess potential population-level effects of licensed control of Cormorants. Although there was an indication that recent declines in the inland population were concurrent with increased control intensity, this can only be considered weak evidence, and such effects may be better considered through intensive research on Cormorant site use and dispersal in relation to control activities. [ABSTRACT FROM PUBLISHER]