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This study examined the effects of the Great Cormorant (Phalacrocorax carbo sinensis L.) roosting colony on the physico-chemical conditions and macrophyte abundance in a shallow soft-water lobelia lake. We compared data collected in 1998 and 2009, before and after 9 years the establishment of a bird colony (2000) along the shoreline of the Lake Dołgie Wielkie (Poland, Europe). Additionally, soils and groundwater beneath the roosting colony were analyzed to evaluate the potential loads of nutrients conveyed to the lake through bird feces. Significant changes in the water quality of the lake were observed in terms of decreased water transparency, and increased conductivity, nitrogen, phosphorus and chlorophyll-a content. Abundance of the more sensitive macrophytes (Littorella uniflora and Myriophyllum alterniflorum) also decreased. At the same time, the occurrence of new, typically meso- and eutrophic macrophytes such as Myriophyllum spicatum and C. demersum was recorded. Soils beneath the bird roosting area were characterized by over 100 fold higher concentrations of nitrogen and phosphorus comparing to not impacted littoral area. Increased nutrient content was also found in the groundwater below the bird colony. The present results suggest that the establishment of the Cormorants colony increases the trophic state of a soft-water lake and affects its macrophyte assemblages.