Freshwater systems are among the most endangered biomes globally. Drivers and pressures include an increased demand for food, energy and water, expansion of urban areas that leads to changes in hydrology and water chemistry, as well as climate change which acts as overarching threat interacting with multiple aspects of the ecosystem. According to the IUCN Red List, 21.5% of assessed freshwater species—a total of >7000 taxa—are threatened. Human influence and threat on aquatic species vary by continent, with Europe having the highest rate of threatened species. Freshwater conservation is challenging as freshwater systems are by definition highly connected entities. Impacts on river health and biodiversity are not localized and often cross administrative boundaries. Management plans need to consider this and trade off services to humans with ecosystem sustainability. Conservation strategies in freshwater systems are varied. Freshwater protected areas exist, but as connected systems they face challenges both in design and governance. Mixed management options such as integrated river basin management are employed to manage multiple threats, especially in larger transboundary rivers such as the Nile, Yangtze or Amazon. Identifying and protecting wild and free-flowing rivers is a preemptive strategy that is gaining traction under the premise that protection of undisturbed habitats is more efficient and effective than restoration. River regulation is a key threat and strategic dam removal or mitigation actions, for example environmental flows can be used to conserve biodiversity—as can targeted catchment reforestation and restoration. All of these strategies need to be embedded in social processes to succeed.