Given the limitations of the short life span and the highly unpredictable environment of branchiopods, a spatial differentiation strategy may become an immediate issue rather than a long-term life history adaptation to potential interspecific competition for a multi-species branchiopod community. We found an ephemeral pool in northern Taiwan with three sympatric branchiopods, Branchinella kugenumaensis (Ishikawa, 1895), Eulimnadia braueriana (Ishikawa, 1895), and Lynceus biformis (Ishikawa, 1895), and thus we aim to explore the spatial distribution patterns among these three species. We measured the density distributions of these species during two inundation episodes (2008P1 and 2008P2) that lasted for 6 and 32 days respectively. Significant differences in both horizontal and vertical distribution of these species were observed. Horizontally, each species showed its own spatial hotspots, but the hotspots changed irregularly every day. Vertically, while B. kugenumaensis gathered in the upper strata, L. biformis spread over a wide range of depths, with increasing dominance towards the deeper layers. Eulimnadia braueriana, on the other hand, showed no significant pattern of vertical distribution due to its small population size. We suggest that the significant differences in the spatial distribution of these sympatric branchiopod populations can be an adaptive strategy under the selective stresses of high unpredictability and variability.