The Watershed Sustainability Index WSI, developed as an integrated method to assess the sustainability of basin management, and particularly water resource management, was applied in the Elqui River Basin over a period offive years (2001-2005). The Elqui watershed is located in a semiarid region of Chile, and it has been incorporated into the River Basin Network of the UNESCO HELP Program. The result was an overall WSI score of 0.61 (within a possible range of 0 to 1), rating the basin sustainability as "intermediate". The main watershed strengths were related to the Environment and Policies indicators. On the other hand, the weakness observed in the watershed was related to the Hydrology indicator, mainly due to water scarcity issues. The bottlenecks and limitations identified in this study represent a window of opportunity to improve the current situation in the basin, and calls for more efficient coordination between the different institutions involved in natural resource management. The application of the WSI in the Elqui basin demonstrated the practicality of the method, both as an analytic instrument, and as a useful management tool for water authorities, water users and stakeholders. An important limitation encountered in this study, however, was a general lack of up to date local information. This needs to be addressed in applying the method for mid- to long-term planning and management strategies, both in the Elqui basin and elsewhere.