The Torrent Duck (Merganetta armata) is one of the four species of ducks that live in fast flowing rivers, and the only one inhabiting mountain rivers from Venezuela to Argentina. This study examines physical-chemical and biological environmental variables associated with different stages of the annual cycle of this waterfowl, to test the relationship between environmental variables and the establishment of territories by Torrent Ducks in the southern part of their range between November 2009 and April 2011. Territories were defined as sites where a pair of Torrent Ducks was found throughout the year, while non-territories were defined as sites where solitary birds were spotted in some seasons but not year-round. The variables that best explained the habitat use by Torrent Ducks were: 1) in spring, the energy of main prey items available per square meter of river, and 2) in fall, the flow rate. Higher food availability in spring and higher water flow in small rivers in fall were associated positively with paired Torrent Ducks' territory establishment. The future assessment of breeding success in territories with contrasting levels of food and water flow may allow for the determination of the importance of these variables for habitat selection, and the meaning that changes in precipitation caused by climate change may have on this species.