Spring surveys of 112 temporary floodplain waters on River Murray tributaries demonstrated a heterogeneous habitat series, with ca. 500 species of microfauna encountered. Rotifers comprised the most diverse group (>250 taxa), however mean diversity was low (10.93 ± 7.5), in part reflecting predation by copepods and macroinvertebrates. Notably, only 10 rotifer species could be considered widespread in the study area. Ephemeral pool microfaunal communities were distinct from those of adjacent permanent billabongs; their community variability is seen as a function of, or response to, habitat heterogeneity. The significance of high species diversity in ephemeral waters is considered in the context of age of the Murray-Darling Basin, which has persisted in its present location since the breakup of Gondwana, >65 MY BP.