New Zealand’s freshwater ecosystems support a diverse and unique array of endemic flora and fauna. However, the conservation of its freshwater biodiversity is often overlooked in comparison to terrestrial and marine environments, and is under increasing threat from agricultural intensification, urbanisation, climate change, invasive species, and water abstraction. New Zealand has some of the highest levels of threatened freshwater species in the world with, for example, up to 74% of native freshwater fish listed as endangered or at risk. Threatened species are often discounted in water policy and management that is predominantly focussed on balancing water quality and economic development rather than biodiversity. We identify six clear actions to redress the balance of protecting New Zealand’s freshwater biodiversity: 1. change legislation to adequately protect native and endemic fish species and invertebrates, including those harvested commercially and recreationally; 2. protect habitat critical to the survival of New Zealand’s rare and range-restricted fish, invertebrate and plant freshwater species; 3. include river habitat to protect ecosystem health in the National Objectives Framework for the National Policy Statement for freshwater; 4. establish monitoring and recovery plans for New Zealand’s threatened freshwater invertebrate fauna; 5. develop policy and best management practices for freshwater catchments in addition to lakes and rivers to also include wetlands, estuaries, and groundwater ecosystems; and 6. establish, improve, and maintain appropriately wide riparian zones that connect across entire water catchments. We have published these recommendations as a scientific statement prepared for the Oceania Section of the Society for Conservation Biology to facilitate communication of our thoughts to as wide an audience as possible (https://conbio.org/images/content_groups/Oceania/Scientific_Statement_1_.pdf, accessed 8 February 2016).