In contrast to surface water ecosystems, groundwater ecosystems are usually considered to have relatively stable conditions and physically inert environments. However, many groundwater ecosystems undergo substantial changes through space and time, related to fluxes in groundwater flow, exchange and nutrient imports.In this study we used hydrochemical data to: 1) determine the different hydrogeological conditions in an alluvial system, the shallow Gwydir River alluvial aquifer (located in Northern New South Wales, Australia); and 2) analyze the relationship between hydrochemical conditions and the composition of stygofauna assemblages in the aquifer.Using hydrochemical modeling and multivariate analyses, four main hydrogeological situations were defined as occurring in the aquifer. Bores were classified as having either a high, low or no influence from or exchange with the river. The latter group was further subdivided into those of low and high salinity.Further analysis combining the biological and hydrochemical data identified two main groups of samples. The first group was composed mainly of samples related to the aquifer groundwater which had higher richness and abundance of fauna compared to samples in the second group which was comprised of samples affected by stream water leakage and samples related to the highest salinities. These results suggest that more stable conditions (mainly related to steadier groundwater head levels) and lower nitrate concentrations promoted a more diverse and abundant stygofauna community.