ABSTRACT1. The Strobel Meseta, a basaltic plateau of Patagonia (Santa Cruz Province, Argentina), holds thousands of shallow fishless lakes that are prime habitat for many species of waterbirds, including some considered 'near threatened'. In recent years, several lakes have been stocked with trout which has created uncertainty about the potential effects on the recipient ecosystem.2. Limnological and topographical analyses were performed in a group of 32 lakes of the Strobel Meseta in order to characterize and classify individual lakes of the meseta based on their limnological and topographic features, analyze the association between lake type and use by aquatic birds in general and by the endemic hooded grebe (Podiceps gallardoi) in particular, and evaluate the overlap between trout aquaculture and critical habitat for waterbirds.3. The lakes were classified by multivariate analyses into four characteristic types: turbid, high conductivity lakes (T), small vegetated lakes (SV) and larger lakes which were subdivided into either vegetated (LV) or unvegetated (LU). In general, macrophyte cover was the main classificatory variable, whereas conductivity, pH, surface, and depth contributed moderately. Large vegetated lakes were generally found to be important for waterbirds and provided critical habitat for the hooded grebe, whereas trout farmers largely favoured large unvegetated lakes. However, since some large vegetated lakes have already been stocked, there is some level of geographical overlap between waterbird habitat and trout farming.4. The existence of some level of spatial segregation between production and critical waterbird habitat affords opportunities for designing a spatially-based management system for trout aquaculture.