Ecologists have recently begun to explore the relationships between the composition of invertebrate assemblages and environmental gradients in groundwater of unconsolidated sediments. Hydrogeological attributes such as permeability expectedly drive biodiversity patterns in groundwater because they not only exert a direct influence on organisms but also control fluxes of nutrients and organic matter. We used the OMI analysis (outlying mean index) to examine the responses of multiple species to hydrogeological and physico-chemical variables in a shallow water-table aquifer along the Loire River, France, the water chemistry of which has been severely affected by gravel extraction and refilling with demolition materials. Hydrogeological attributes were obtained from a finite-difference groundwater flow model whereas physical variables and biological data (i.e. presence – absence of species) were collected during a single survey of 29 wells. Groundwater had elevated concentrations of dissolved organic carbon (DOC) and contained a high number of species, among which a majority was epigean. Spatial variation in physico-chemistry of groundwater induced by the dissolution of buried demolition materials had no detectable influence on the distribution pattern of fauna. Rather, species were significantly distributed along an environmental gradient defined primarily by permeability and vadose zone thickness. These variables had in turn a detectable influence on groundwater temperature and concentrations of DOC and total dissolved solids. Our results emphasize the importance of integrating hydrogeological measurements within the framework of ecological studies for understanding distribution patterns of invertebrate assemblages in groundwater.