Management of water resources needs to jointly consider the multiple, interdependent, uses of water. Decision support tools that aim to assist efficient integrated water resources management should integrate the environmental and socio-economic systems affected by changes in resource allocation. There exist, however, few models that assess the trade-offs between environmental and economic impacts of water management changes in an integrated framework. This paper presents a hydro-economic model that integrates hydrological and ecological systems with economic costs and nonmarket benefits in a Bayesian Network modelling framework. A suite of different modelling tools were used to assess the biophysical and economic impacts of catchment management scenarios, for a case study in Tasmania, Australia. The Bayesian Network provides a flexible modelling approach to incorporate different types of data and had the advantage of explicitly accounting for accumulated uncertainty in information.