Drought is a constant and important consequence of natural climatic processes and most freshwater fishes have adaptations to counter its effects. However, a changing global climate coupled with increasing human demand for water is reducing the availability of fresh water to fishes and contributing to more frequent and intense drought around the globe. A clear understanding of how fishes, fish habitat, and fisheries are affected by extended drought is needed to help resolve conflicts over water. We therefore identify key questions and research themes to promote the conservation of freshwater fishes as drought increases in length, frequency and severity. (1) How does drought affect fish habitat? (2) What is drought tolerance in fishes? (3) What are drought refuges for fishes? (4) What kills fish during drought? (5) What is the nature of species succession in drought-stricken waters? (6) What are the long-term consequences of drought to fishes? (7) How does climate change affect drought-fish interactions? (8) How does drought influence fisheries? Our limited ability to provide answers to these questions indicates that fish diversity and abundance worldwide is threatened by drought. Planning, including collection of long-term data, is necessary so that conservation and water re-allocation strategies can be implemented in a timely manner to maintain habitats necessary to support biodiversity during drought periods. Without increased understanding of physiological and behavioural factors that determine the tolerance of fishes to drought, it will not be possible to establish realistic targets for management and restoration of populations and species confronting increasing drought frequency and severity.