Seasonal (semestral) counts of aquatic birds at five Andean lakes in Ecuador (Colta, La Mica, Yambo, Yahuarcocha and San Pablo) were analyzed to detect trends in population size between 2004 and 2011. Trends of four abundant species (Ardea alba, Anas georgica, Fulica ardesiaca and Oxyura jamaicensis) and those of five functional groups (based upon body size and diet) were tested using generalized additive mixed modeling. In total, 19 bird species were consistently recorded over the whole period. The Andean Coot (F. ardesiaca) was found in highest densities (c. 3 birds per ha at Colta and Yambo). No significant trends were detected. However, the counts of functional groups exhibited a seasonal pattern (higher counts in February than in July), possibly due to lower resource availability in the dry season. Piscivorous species were relatively abundant at one lake (Yahuarcocha), which might be related to the introduction of Tilapiine cichlid fishes.