Development of an Assessment System to Evaluate the Ecological Status of Rivers in the Hindu Kush-Himalayan Region (ASSESS-HKH) was a 3-year research project funded by the European Union (Contract number: INCO-CT-2005-003659). This article provides an overview of this research project by summarising the objectives, the approaches and the main achievements. The main objective was to develop and apply a biological assessment system to evaluate the river’s ecological quality and to provide a scientific basis for the identification of sustainable water policy options and management strategies. The assessment tools were jointly developed by European partners, who provided their experience from recent research activities (STAR, AQEM) and Asian partners, who provided the knowledge about Asian river catchments and management necessities. The project was organised into eight work packages defining the time line for all phases, such as establishment of a stream typology and definition of reference conditions and stages of impairment classes for the rivers in the Asian countries, including a review of existing policies for water management. A specific part of the project was dedicated to increasing the overall poor knowledge of benthic invertebrates in the region and their value to the classification of the river’s ecological quality. All activities were accompanied by information events for local residents, universities and water managers. A total of 396 multi-habitat samples, from 115 rivers in five different ecoregions, were taken in two different seasons and accompanied by information on 95 parameters describing river and catchment characteristics. The benthic invertebrates in the samples were taxonomically identified based on keys generated within the project. Taxalists, with abundances per site, and field protocol information were entered into a specifically developed software tool. This dataset was the basis for developing ecological river assessment methods, called HKHscreening (Rapid Field Assessment), HKHbios (HKH Biotic Score) and HKHindex (Multimetric Index). Furthermore, a software tool (ECODAT) for using these methods was developed. The monitoring tools will serve citizens and scientists of the Hindu Kush-Himalayan region and will provide a scientific basis for policy recommendations, mitigation strategies, transnational water resource planning and sustainable ecosystem management. Additional outputs, including all sampling and laboratory protocols and project deliverables, together with the freely downloadable software, are available at the following website: http://www.assess-hkh.at.