1. Growing recognition of the ecological significance and biodiversity of groundwater fauna in Australia has led to statutory requirements for monitoring these communities prior to resource development. However, the efficiency of methods for assessing community composition and taxa richness remains untested, hampering the collection of reliable data for compliance. 2. We assessed the efficiency of two commonly-used methods to sample groundwater fauna (net hauls and pumping) in bores in two contrasting regions (Dubbo and upper Hunter Valley) of eastern Australia. Repeated sets of seasonal samples from the upper Hunter Valley bores were used to test whether once-off sampling was sufficient for compliance purposes. 3. All taxa collected by the net method were also captured in pump samples. In addition, pumping yielded more taxa, higher total abundances, and higher numbers of the two most common taxa (syncarids and copepods) than the net. Ten net hauls in the upper Hunter Valley bores collected, on average, 64% of the taxa and 44% of total abundance. When combined with the first 100 L from pumping, cumulative totals rose to 92.5% and 74.5% respectively. Similar trends occurred in bores near Dubbo, indicating that net hauls alone under-sampled groundwater faunal communities. Multivariate analyses revealed substantial differences in community composition as each incremental subsample was added. 4. Temporal changes in community composition in the Hunter Valley aquifer were marked yet inconsistent across the bores. Initial once-off sampling collected 30–87% of the total taxa from each bore and new taxa were still being collected after four sampling periods in over half the bores. This shows that more than one sampling occasion is needed for comprehensive assessments of groundwater biodiversity. 5. Successful compliance monitoring of groundwater fauna requires cost-effective sampling that will not overlook potentially vulnerable taxa or miss ecologically relevant changes in community composition. Currently, a lack of suitable bores seems to be the main constraint on accurate assessment of groundwater invertebrate community composition in these two areas of eastern Australia.