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Waterbirds are one of the most important groups of organisms inhabiting the land–water interface, especially with regard to mediating the transport of materials from the aquatic to the terrestrial environment. The great cormorant ( Phalacrocorax carbo) is a colonial piscivorous bird that transports nutrients from fresh water to forest. We measured cormorant-derived nitrogen at two nesting colonies on the Isaki Peninsula and Chikubu Island at Lake Biwa, Japan, and analyzed the long-term effects of cormorant colonization on the forest nitrogen cycle, and the mechanisms of nitrogen retention. Three sites were examined in each colony: a currently occupied area, a previously occupied but now abandoned area, and a control area never colonized by cormorants. High nitrogen stable isotope ratios of cormorant excreta, the forest floor, mineral soil, and living plants showed cormorant-derived nitrogen in both occupied and abandoned areas. The relationship between δ15N and N content showed that the high δ15N of the excreta and N turnover in the soil were important at the occupied sites, whereas high δ15N of litter was important at the abandoned sites. Physiological changes of various organisms are also important for the N decomposition process. In conclusion, cormorant-derived nitrogen remains in the forest ecosystem as a result of two cormorant activities: heavy deposition of excreta and collection of nitrogen-rich nest material. Colony stage (occupied, abandoned, or never inhabited) and historical change of N decomposition process of an area can be identified from the relationship between δ15N and N content. [ABSTRACT FROM AUTHOR]