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In the Laurentian Great Lakes region, the double-crested cormorant (Phalacrocorax auritus) has seen a thousand-fold population increase in recent decades. These large colonies of birds now often conflict with socioeconomic interests, particularly due to perceived competition with fisheries and the destruction of terrestrial vegetation in nesting habitats. Here we use dated sediment cores from ponds on islands in eastern Lake Ontario that receive waste inputs from dense colonies of cormorants and ring-billed gulls (Larus delawarensis) to chronicle the population rise of these species and assess their long-term ecological impacts. Modern water chemistry sampling from these sites reveals drastically elevated nutrient and major ion concentrations compared to reference ponds not influenced by waterbirds. Geochemical tracers in dated sediment cores, particularly δ15N and chlorophyll-a concentrations, track waterbird influences over time. Fossil diatom assemblages were dominated by species tolerant of hyper-eutrophic and polluted systems, which is in marked contrast to assemblages in reference sites. In addition to establishing long-term ecological impacts, this multi-proxy paleoecological approach can be used to determine whether islands of concern have been long-term nesting sites or were only recently colonized by cormorant or ring-billed gull populations across the Great Lakes, facilitating informed management decisions about controversial culling programs.

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