The abstraction of groundwater is a global phenomenon that directly threatens groundwater ecosystems. Despite the global significance of this issue, the impact of groundwater abstraction and the lowering of groundwater tables on biota is poorly known. The aim of this study is to determine the impacts of groundwater drawdown in unconfined aquifers on the distribution of fauna close to the water table, and the tolerance of groundwater fauna to sediment drying once water levels have declined. A series of column experiments were conducted to investigate the depth distribution of different stygofauna (Syncarida and Copepoda) under saturated conditions and after fast and slow water table declines. Further, the survival of stygofauna under conditions of reduced sediment water content was tested. The distribution and response of stygofauna to water drawdown was taxon specific, but with the common response of some fauna being stranded by water level decline. So too, the survival of stygofauna under different levels of sediment saturation was variable. Syncarida were better able to tolerate drying conditions than the Copepoda, but mortality of all groups increased with decreasing sediment water content. The results of this work provide new understanding of the response of fauna to water table drawdown. Such improved understanding is necessary for sustainable use of groundwater, and allows for targeted strategies to better manage groundwater abstraction and maintain groundwater biodiversity.