In many developing countries, natural resource management is based on traditional, expert-based methods that often exclude a variety of stakeholders. This paper presents a conceptual model and methodology that represent a first step toward a more integrated evaluation and management of large basins. The main objective of this paper is to evaluate the socioeconomic impact of the application of secondary water quality regulations in the Aysen River Basin of Southern Chile. We employ the concept of physical, ecological and social (PHES)-system as a conceptual framework. Three indices based on this framework were created to characterize different aspects of the Aysen Basin: an environmental vulnerability index, an index of the water quality impact of the different economic sectors, and an index that quantifies the economic contribution of these sectors. Finally the three indices were combined as a measure of the socioeconomic impact of the proposed regulations in what we referred to as the 'applied assessment model'. Our results suggest that the applied regulations would have little socioeconomic impact on the Aysen Basin. Finally we discuss challenges to integrated watershed assessment in the context of developing countries.