Gradients in the sediment fauna comprising groundwater (GW) and hyporheic taxa were investigated in the sand/silt-bottomed Marbling Brook in Western Australia. The structure of sediment invertebrate assemblages from Marbling Brook sediments and the adjacent GW were studied at five sites over 1 year and hydrological interactions were characterized using a suite of abiotic factors. Although all five stream sites were upwelling, the sites differed in the degree of hydrological interactions between GW and surface water. Sediment fauna taxa abundances were not correlated with any of the abiotic factors investigated and did not change gradually with depth. Faunal assemblages in the stream sediments were distinct from faunal assemblages in alluvial GW. While water exchanged between alluvial GW and sediment water, as shown by abiotic factors, the distinct differences in faunal assemblages indicated an unpredicted complexity in the catchment with fundamentally different hydrogeological situations on the decimetre scale. Sampling in sandy sediments needs to take this small-scale variability into account.