The nature of spatial autocorrelation of biota may reveal much about underlying ecological and biological factors responsible for producing those patterns, especially dispersal processes (drift, adult flight, etc.). We report here on assemblage-level autocorrelation in the benthic-invertebrate assemblages (retained in sieves of 300 µm mesh) of riffles in two adjacent, relatively pristine rivers in southeastern Victoria, Australia (40-km reaches of the Wellington and Wonnangatta Rivers). These are related to patterns of autocorrelation in physical and catchment conditions (‘environmental variables’) in the vicinity of the sampling points. Both the invertebrate assemblages and environmental variables were autocorrelated at small scales (= 8 km) in the Wellington River in one of the sampling years (1996). Dissimilarities of invertebrate assemblages were correlated with dissimilarities of environmental variables in both sampling years (1996 and 1997) in that river. Environmental variables were autocorrelated in the Wonnangatta River, but this was not expressed as autocorrelation in the assemblages of invertebrates, which were not autocorrelated at any scale studied. Individual environmental variables showed different spatial patterns between the two rivers. These results suggest that individual rivers have their own idiosyncratic patterns and one cannot assume that even similar, geographically adjacent rivers will have the same patterns, which is a difficulty for ecological assessment and restoration.