Expert systems are typically developed to solve unclear application fields or problems. Such is the case for Chilean river ecosystems, and their fish fauna. In Chile, fish fauna studies are led almost exclusively by biologists, but no or Little information is available about reproductive season, fertility, reproductive strategies, age, locomotive capacity, migration, trophic dynamic or niche, to name a few. Quantitative studies are required to analyse the impact of exotic over native species and the antropic effect over a population's decrease. This information is essential to take appropriate conservation measures for each species and aquatic system. On the other hand, the lack of an adequate hydrometric network forces the use of complementary tools that introduce uncertainties, which are expensive and of difficult quantification. Due to the absence of gauged data for the study area, an expert system application methodology was coupled to the hydrological and hydraulic models, GR4J and HEC-RAS, respectively. Fish species information was taken from biological studies performed for the basin of the Bio Bio River where 17 fish species (13 native and 4 exotic, were found); furthermore, 7 species are classified as vulnerable and 7 are endangered. Conclusions are focused on the methodology as well as on information quality and source. The research indicated that habitat modelling efforts would be strongly limited by Chile's unclear environmental policy, including lack of data in all areas for an environmental study. Chile's capacity to adopt holistic tools for water resources management is commented. The study concludes with recommendations for improving the integration of environmental policy issues into Chile's water resource management. Copyright © IAHS Press.