Large river ecosystems worldwide are under increasing pressures from environmentally degrading processes related to population increase,land use changes, climate change and the release of chemical substancesinto the environment. The large spatial scale and a lack of empiricaland theoretical understanding of the systems complicate environmental assessment in these systems. Recently, the Northern River Basins Study(NRBS) undertook a multi-disciplinary approach to assess environmentaland socio-economic impacts of development in three large river basins,the Peace, Athabasca and Slave river basins in northern Canada. This paper provides the background and context for the NRBS and describes therationale used in developing an assessment framework for the Study. An independent science advisory committee comprised of scientific experts from academia, First Nations and government oversaw quality assurance interms of science planning, implementation and reporting. All technical studies were subject to both internal and external peer review prior to approval by a multi-stakeholder Study Board. The NRBS produced over 150 technical and 12 synthesis reports that detailed these findings andprovided scientific recommendations. The Study Board used this information to prepare a final report and recommendations. The NRBSprovides a clear example of a participatory, stakeholder approach that was successfully implemented in the design and management of an integrated watershed environmental assessment program.