Water catchments are functional geographical areas that integrate a variety of environmental processes and human impacts on landscapes. Integrated assessments recognize this interdependence of resources and components making up water catchments and are vital for viable long-term natural resource management. This paper couples eco-hydrological modelling with remote sensing, landscape ecological analyses and GIS to develop a series of indicators of water catchment health as part of a geographical audit of environmental health and change at regional scales. Indicators are simple measures that represent key components of the system and have meaning beyond the attributes that are directly measured. A suite of indicators, many capable of measurement from remote sensing data sources, are described that represent state (condition) and trend (changes across space and time) and focus on the physical, biological and chemical properties of water catchments, as well as their ecological function (stability, resilience, and sensitivity). Models implemented in GIS allow indicators to be combined within water catchments by setting them within a specific geographic context and integrating the descriptions of environmental variability across the geographic area. This spatial integration is necessary to place individual, site-specific indicators within a broader geographic context; the models allow this context to reflect the ecological and hydrological functioning of the water catchment. Scale and other geographic effects associated with integration are managed using an approach that partitions the landscape into a hierarchical series of nested functional units. Methods from image analysis, landscape ecological analysis, spatial interpolation, and numerical process modelling are integrated within a GIS (ArcView) to provide a single environment within which to conduct the study. Results are described from the catchment of the upper Yellowstone River in the Rocky Mountains, USA, an area of about 14 000 km2. The river source is in Yellowstone National Park. The catchment is subject to a number of land-use issues notably those associated with changing patterns and types of land use including forestry, irrigated agriculture, range management, wildfire, mining, summer and winter recreation, and residential development, which are associated with a number of land-use conflicts and impacts.