In the Australian sub-tropics, seasonal changes in hydrology can influence abiotic conditions, and consequently, the biota. Several methods of macroinvertebrate analyses, including the use of taxonomic groupings, are used to ascertain information regarding stream biodiversity and health. The use of biological traits to group and analyse macroinvertebrate communities, however, may provide a better picture of stream health, particularly in ephemeral streams. To address whether this is the case, three ephemeral systems in the lower Fitzroy catchment, Central Queensland, Australia, were studied over an 18-month period. A total of 69 macroinvertebrate families from 14 orders were collected in 128 samples. Taxonomic analysis indicated there was a range of habitat preferences within groups characterized by a large proportion of tolerant and generalist taxa. The macroinvertebrate communities were categorised into biological trait groups, with a number of predator families found during all flow regimes. A general pattern of Gatherer > Predator > Grazer > Shredder > Filterer was observed. This study provides a clear pattern of the biological traits present during variable flow and could be used as a framework for future stream health modelling. A trait-specific management tool for assessing freshwaters has not yet been adopted in global management protocols and would require both a more definitive understanding of patterns during different flow periods and an internationally recognised set of trait nomenclature.