Ephemeral streams are waterways with poorly defined channels and episodic flow. Globally, the occurrence of ephemeral streams appears to be increasing due to drying trends driven by climate change, as well as a result of increased water abstraction rates. Simultaneously, these pressures will also result in increased vulnerability of ephemeral streams, as flow rates decline from intermittent to entirely absent. Despite this, ephemeral waterways are broadly neglected by ecologists, and no tailored measures are available to study the health of these systems. Traditional assessment methods for lotic or lentic environments include physicochemical analyses, often teamed with the use of biological indicator species. Of the latter, macroinvertebrates are widely favoured because of their abundance and diversity, as well as their sensitivity to changes in flow, water quality and toxic impacts. However, the theoretical base that underpins macroinvertebrate protocols has generally been developed from studies of temperate, permanent waterways. In contrast, hardly any studies that contributed to the development of bio-assessment approaches specifically related to (tropical/subtropical) ephemeral environments. This review examines the current state of knowledge regarding the health of ephemeral systems and applicable ecosystem health measures that may be transferable to ephemeral systems, with a particular focus on macroinvertbrates as bioindicator species.