Guanay Cormorant populations fluctuate greatly with climatic changes, especially powerful El Niño events (Jordan 1966). In a year with a strong El Niño, the upwelling along the coast declines or ceases entirely, causing a fish population crash. In response, cormorants will abandon nests and disperse far to the north and south in search of food. Millions usually starve (Duffy 1983b).
Population estimates range from < 4 million from 1909 to 1920, to 21 million in 1954 and 1955, to 3.7 million in the same region in 1996 (Zavalaga and Paredes 1999).
Cormorants are afflicted by a number of ectoparasites, including the lice Eidmanniella pellucida and Piagetiella transitans (Sepulveda 1997). The argasid tick (Ornithodoros amblus) can cause nest desertion in years with large tick populationss (Duffy 1983d).