Growing evidence suggests that freshwater ecosystems incur exacerbated impacts during drought due to anthropogenic activities. This has prompted calls for the development of drought management strategies that more effectively incorporate these ecosystems. Efforts to examine how drought management instruments care for freshwater ecosystems are scarce, limited to a few geographic regions, and do not systematically analyse each of the elements of the drought management process. In this study, we review drought management instruments in 26 countries or regions within countries to assess the extent and the manner with which freshwater ecosystems are considered. We apply an analytical framework integrating knowledge from drought management, ecological risk assessment and ecological drought to extract data from these instruments and identify patterns and gaps. Results indicate that care for freshwater ecosystems in drought management is as yet at an early stage. This is reflected in the limited inclusion of freshwater ecosystems across critical elements of the drought management process, as well as significant shortcomings in how these ecosystems are considered. We synthesise these shortcomings in four gaps. First, the socio-ecological perspective of ecological drought, particularly regarding the combined natural-human causes of drought impacts on freshwater ecosystems, is often lacking in drought definitions, exposure and vulnerability assessments. Second, despite their importance to ecosystems, there is limited consideration of variables related to groundwater, water quality, and aquatic habitats in freshwater ecosystem indicators, exposure assessments and measures. Third, the duration, frequency and timing of drought, which are relevant to the ecology of freshwater ecosystems, are rarely considered in drought indicators and measures. Finally, exposure and vulnerability assessments often lack a comprehensive understanding of ecological drought risk in freshwater ecosystems. We discuss these gaps and provide an outlook towards more integrated and sustainable drought policy and management.