Calcrete aquifers are unique groundwater habitats containing stygobiontic species endemic to each calcrete. The evolutionary history of stygofauna suggests the calcretes in Western Australia contain multiple ancient lineages, yet populations experience episodic variation in rainfall patterns, with little-known ecological consequences. The aim of the present study was to document stygofaunal diversity patterns and determine whether they are influenced by rainfall events. The average taxon richness in boreholes peaked shortly after periods of high rainfall, and when dominant taxa were excluded, evenness decreased after periods of both high and low rainfall, indicating that dominant taxa are an important factor in driving the system. Strong abundance-distribution relationships reflected the commonality of taxon groups; common taxon groups had broad distributions and high abundance levels, whereas rare taxon groups had small distributions and low abundance. After periods of intermediate and low rainfall, taxon groups had narrower distributions and the maximum number of individuals per borehole was lower. Finally, the majority of boreholes did not show changes in evenness over the 11-year study period, suggesting a reasonably stable ecosystem with episodic fluctuations that can be attributed to rainfall events. The results of the present study indicate that diversity patterns within boreholes are driven episodically by both external and internal factors, such as rainfall and rapid borehole dominance respectively.