The nutrients imported by breeding waterbirds should be considered when identifying the main sources of nutrient input to lakes. Lake Lesser Prespa (Greece), including the adjacent Vromolimni pond, hosts numerous protected waterbirds that nest in densely populated colonies across the reedbeds. The accelerated eutrophication of the lake in recent years has been of increasing concern. In addition to likely large sources of nutrients (i.e., anthropogenic activities, especially agriculture), nutrient input via waterbird excrement may further trigger eutrophication. We estimated the annual phosphorus (P) and nitrogen (N) input by the most abundant colonial-nesting waterbirds (great white pelican, Dalmatian pelican, great cormorant, and pygmy cormorant) into the lake and investigated their influence on water and sediment quality. Near the waterbird colonies, soluble nutrient concentrations in the lake sediments were higher, and chlorophyll measurements indicated higher algal growth near these sites in summer. Stable isotope analysis suggests that near the colonies, waterbirds are responsible for nutrient loadings that affect the lake sediment. The estimated N and P nutrient input into the lake by both pelican and cormorant species is at least 1243 and 1649 kg/yr, respectively. On a landscape scale, this level of loading could be of minor importance for the lake because N and P can reach 32.8 (SD 9.3) and 38.9 (5.8) mg/m2 per year, respectively. Locally, however, this level of loading might induce cyanobacterial blooms, illustrated by the analysis of isolated Vromolimni pond near the lake. Our findings emphasize the likely importance of nutrient loading by waterbirds for the lake system.