The Torrent Duck (Merganetta armata) inhabits the torrential rivers of the Andean mountains. As part of a long-term study, two rivers important for hydroelectric production were surveyed in Central Chile. Monthly indices of Torrent Duck abundance and reproduction were recorded at 74 sampling points distributed along 35.4 km of river between 2007 and 2009. Habitat variables were measured to determine the factors that influence species abundance. The number of rapids, gradient, total flow, water velocity, relative position to hydropower intakes and abundance of conspecifics were identified as important attributes in Torrent Duck habitat preferences. Torrent Ducks were observed in selected sections of rivers where the presence of rapids, high slopes and high water velocity occurred. These conditions were influenced by the width and shape of the river bed. Spatial segregation among individuals suggests the effect of territoriality. Torrent Ducks tended to avoid the presence of high vehicular traffic roads and sections downstream of the hydropower intakes. The hydropower intakes showed no impact on either the chemistry of the water or the composition of the macroinvertebrate community. The negative effects of hydroelectric power production on Torrent Duck populations could be mitigated through the modification of the shape of the river channel.