Freshwater is a key resource and medium for various economic sectors and domestic purposes but its use is often at the expense of natural ecosystems. Water management must change to deal with urgent issues and protect aquatic ecosystems and their services, while addressing the demand for water from the competing claims for cities, agriculture, industry, energy and transport. In this paper key water challenges (shortage, pollution, aquatic ecosystems threatened) have been identified via global modelling. By the IMAGE-GLOBIO model chain a Trend scenario up to 2050 was modelled, as well as the potential of three ‘pathways’ aimed at halving average global biodiversity loss while also meeting the sustainable development goals. Biodiversity is then used as a guiding principle to address these challenges because water services depend on healthy and biodiverse ecosystems. Subsequently the potential of nature-based solutions is reviewed for four sub-sectors: cities, food production, hydropower, and flood protection, grouped under the three alternative pathways to meet key water challenges. Mainstreaming biodiversity into water policy requires integrated planning. Integrated Water Resource Management (IWRM) could provide an opportune starting point as a well recognised integrating framework for planning, to guide the actual implementation of nature-based solutions in sub-sectors.