Mongolia is not only a water-scarce but also a data-scarce country with regard to environmental information. At the same time, regional effects of global climate change, major land use changes, a booming mining sector, and growing cities with insufficient and decaying water and wastewater infrastructures result in an increasingly unsustainable exploitation and contamination of ground and surface water resources putting at risk both aquatic ecosystems and human health. For the mesoscale (≈15,000 km²) model region of the Kharaa River Basin (KRB), we investigated (1) the current state of aquatic ecosystems, water availability and quality; (2) past and expected future trends in these fields and their drivers; (3) water governance structures and their recent reforms; and (4) technical and non-technical interventions as potential components of an integrated water resources management (IWRM). By now, the KRB is recognized as one of the most intensively studied river basins of the country, and considered a model region for science-based water resources management by the Mongolian government which recently adopted the IWRM concept in its National Water Program. Based on the scientific results and practical experiences from a six-year project in the KRB, the potentials and limitations of IWRM implementation under the conditions of data-scarcity are discussed.

A comprehensive monitoring project (2006–2013) provided data on hydrology, hydromorphology, climatology, water physico-chemistry, sedimentology, macroinvertebrate community and fish diversity in the Kharaa River basin in northern Mongolia, thus enabling, for the first time, a detailed characterization of the stream landscapes. Surface waters were categorized into separate “water bodies” according to their identifiable abiotic and biocoenotic features, subsequently creating the smallest management sub-units within the river basin. Following the approach of the European Water Framework Directive (EC-WFD), in order to obtain a good ecological status (GES), four clearly identifiable water bodies in the Kharaa River main channel and seven water bodies consisting of the basin’s tributaries were delineated. The type-specific undisturbed reference state of various aquatic ecosystems was identified in the assessment and used to set standards for restoration goals. With regards to water quality and quantity, the upper reaches of the Kharaa River basin in the Khentii Mountains were classified as having a “good” ecological and chemical status. Compared with these natural reference conditions in the upper reaches, the initial risk assessment identified several “hot spot” regions with impacted water bodies in the middle and lower basin. Subsequently, the affected water bodies are at risk of not obtaining a level of good ecological and/or chemical status for surface waters. Finally, a matrix of cause-response relationships and stressor complexes has been developed and is presented here. The applicability of management approaches is discussed to better foster the development of a sustainable river basin management plan. The application of natural references states offers a sound scientific base to assess the impact of anthropogenic activities across the Kharaa River basin.