Because of their remote location and lack of supporting infrastructure, large glacial rivers of southern Patagonia have remained free of dams. But this is bound to change: two dams proposed for the Santa Cruz River would supply 16% of Argentina's hydropower and five dams planned for the Pascua and Baker Rivers could supply over 20% of Chile's hydropower. In this paper, we project the losses of habitat and juvenile Oncorhynchus mykiss, a recreationally important species, following the construction of the two dams in the Santa Cruz River. We applied a two-stage fitting approach, using generalized additive models and generalized lineal models (GLMs) sequentially to describe habitat-species relationships based on data collected through an intensive field survey of fish and environmental variables along 310 km of river. A simplified GLM trout model based on wetted width, substrate size, and river kilometer was selected which represents the observed geographic distribution very well and with the lowest predictive error. Based on this model, we estimated that habitat supporting 86% of current juvenile trout production will be lost to flooding by the dams. Our data generate a rare opportunity to perform a dam impact assessment by comparison with potential post-dam conditions.