Abstract: The way we manage water in the rangelands affects the plants and animals that are largely dependent on water supply, quality and seasonal variability. Here, we identify five issues of national significance that are affecting water and biodiversity. They are climate change, modified natural flow regimes, leaky landscapes, artificial water points, and tourism and recreation. Sustainable management practices are crucial to preserving flora and fauna biodiversity. As yet, no rigorously tested best management practices have been developed for managing water to conserve biodiversity in the rangelands. Principles on which to base best practices are as follows: – Avoid adverse environmental effects of activities. – Fix any problems that have or are likely to occur. – Mitigate any effects that are either unavoidable or cannot be fixed. – Protect or restore threatened or significant ecosystems; this makes them more resilient and capable of dealing with changes in their environment. – Maintain natural flow regimes in rivers, wetlands and aquifers. – Allocate water to human use in proportion to natural flow. Undertake a whole-of-catchment analysis before implementing policies for protecting or extracting water. The single greatest knowledge gap is the lack of an integrated understanding of the ecology of Australia’s inland waters, and the effects on these inland waters of changes through water extraction and grazing, and climate change. Other issues of national significance are threatened species that depend on aquatic habitats for survival; threatened communities such as the mound springs of the Great Artesian Basin; ecological refuges, all of which need to be managed; and uncapped bores and drains. This paper is part of a series of related publications, Managing for Biodiversity in the Rangelands, intended to provide government agencies, land managers and others with relevant information on protecting biodiversity in the rangelands.