Regular counts from 2005 to 2009 were made of the waterbirds inhabiting lakes and ponds in Lanín National Park in the southwestern part of Neuquén Province, Argentina, a landscape dominated by Andean–Patagonian wetlands and forests. Bird surveys conducted on 21 wetland areas detected 8,311 individuals belonging to 27 species from 9 families. The most abundant and frequent species were Ashy-headed Goose (Chloephaga poliocephala), Speckled Teal (Anas flavirostris), Red-gartered Coot (Fulica armillata) and White-winged Coot (Fulica leucoptera). The presence and abundance of bird species with respect to wetland surface area was examined. Small lakes (<100 ha) had higher numbers of individuals, but some species such as the Neotropic Cormorant (Phalacrocorax olivaceus), Great Grebe (Podiceps major), Flying Steamer Duck (Tachyeres patachonicus) and Spectacled Duck (Anas specularis) were more abundant at larger lakes. Speckled Teal, Red Shoveler (Anas platalea) and Chiloe Wigeon (A. sibilatrix) were more common in small- and medium-sized lakes. Most waterbird species were found at a smaller percentage of the lakes where mink were present than at mink-free lakes. Although the ponds and lakes studied are protected within the network of this Argentine National Park, such protection is not implemented effectively. Hence, their future conservation faces several potential threats such as American mink expansion, tourism, fishing and hunting. This information could contribute to the development of management guidelines for the effective conservation of Patagonian wetlands.