There has been an increase in the number of studies examining the spatial and temporal patterns in species richness, community structure and population dynamics of groundwater organisms. These studies have raised the issue of uncertainty about the comparability of different sampling methods, and questions of whether sampling bias may exist. Recently, a diverse subterranean fauna was discovered in calcrete (carbonate) aquifers of the Yilgarn Region of central Western Australia. Little is known about the community structure and population dynamics in these aquifers. One important issue is whether current sampling methods adequately sample the species richness and abundance of the fauna to allow for comparative studies. Here we investigate the effectiveness of three sampling methods: haul net sampling, pumping with a 12-V impeller pump, and a discrete interval sampler. The methods were trialled over 16 months with >250 samples taken from 55 uncased bore holes. No significant taxonomic bias was detected across the sampling methods. However, sampling using a haul net was found to be the most efficient method for capturing the available taxa per unit time when sampling bores are less than 10 m deep, with pumping being the least efficient. These results are discussed in relation to the problems of studying stygofauna in Western Australian calcrete aquifers, and of groundwater faunas more generally.