Freshwater habitats occupy <1% of the Earth's surface, yet are hotspots that support ∼10% of all known species, and ∼⅓ of vertebrate species. Fresh waters also are hotspots for human activities that have led to widespread habitat degradation, pollution, flow regulation and water extraction, fisheries overexploitation, and alien species introductions. These impacts have caused severe declines in the range and abundance of many freshwater species, so that they are now far more imperiled than their marine or terrestrial counterparts. Here, we review progress in conservation of freshwater biodiversity, with a focus on the period since 1986, and outline key challenges for the future. Driven by rising conservation concerns, freshwater ecologists have conducted a great deal of research over the past 25 y on the status, trends, autecology, and propagation of imperiled species, threats to these species, the consequences of biodiversity loss for ecosystem functioning, metapopulation dynamics, biodiversity hotspots, reserve design, habitat restoration, communication with stakeholders, and weaknesses of protective legislation. Nevertheless, existing efforts might be insufficient to stem the ongoing and coming multitude of freshwater extinctions. We briefly discuss 4 important challenges for freshwater conservation. First, climate change will imperil both freshwater species and human uses of fresh water, driving engineering responses that will further threaten the freshwater biota. We need to anticipate both ecological and human responses to climate change, and to encourage rational and deliberate planning of engineering responses to climate change before disasters strike. Second, because freshwater extinctions are already well underway, freshwater conservationists must be prepared to act now to prevent further losses, even if our knowledge is incomplete, and engage more effectively with other stakeholders. Third, we need to bridge the gap between freshwater ecology and conservation biology. Fourth, we suggest that scientific societies and scholarly journals concerned with limnology or freshwater sciences need to improve their historically poor record in publishing important papers and influencing practice in conservation ecology. Failure to meet these challenges will lead to the extinction or impoverishment of the very subjects of our research.