Springs are important freshwater habitats that provide refuge for many rare species. In this study, the fauna and abiotic parameters of 20 perennial springs in north-western Switzerland were investigated. Correlation of abiotic and macrozoobenthos data showed that physicochemical parameters had little impact on macrozoobenthic composition, whereas specific substrate parameters strongly influenced the composition of the macrofauna. Surprisingly, nonmetric multidimensional scaling did not reveal a grouping of springs with similar substrate composition or macrozoobenthic assemblages. However, discharge was identified as the factor significantly determining substrate and the composition of macroinvertebrate assemblages. This justifies the hypothesis that, variation in discharge is the disturbance factor governing the macrofaunal composition temporally and spatially within and between patches.