The relation between environmental conditions and the species composition and individual abundance of crustaceans was investigated in a shallow alluvial aquifer, located in the Danube wetlands (Lobau, Austria). Samples, consisting of groundwater, sediment, and fauna, were taken from permanent installed wells by means of a piston pump five times in a year cycle.The results show that the spatial and temporal distribution, individual abundance, and species richness of crustacean fauna is related to hydrological conditions, oxygen concentrations, and geologic structures in the alluvial aquifer. Therefore, crustaceans, divided in stygoxene, stygophile, and stygobite species, can be used as bioindicators of these environmental conditions in an aquifer. It is suggested that beside physicochemical analyses also the crustacean fauna should be considered to characterise a groundwater ecosystem.