Understanding how spatial variability in stream discharge and water chemistry decrease with increasing catchment area is required to improve our ability to predict hydrological and biogeochemical processes in ungauged basins. We investigated differences in this decrease of variability with increasing catchment area among catchments and among specific discharge (Qs) and water chemistry parameters. We defined the slope of the decrease in the variability with increasing catchment area as the rate of decrease in the standard deviation and coefficient of variation (δSD and δCV, respectively), both of which are −0.5 for the simple mixing of random variables (random mixing). All δSD and δCV values of Qs were less than −0.5, while those of most water chemistry values were greater than −0.5, indicating that with increased catchment area the spatial variability of Qs decreased more steeply than for random mixing, while for water chemistry they decreased less steeply. δSD and δCV had linear relationships with both the spatial dissimilarity index and relative changes in parameters' mean values with increasing catchment area. It suggested that differences in δSD or δCV for Qs and water chemistry can be explained by the different spatial structures, where dissimilar values of Qs and similar values of water chemistry, respectively, are located close together in space. Differences in δSD and δCV according to Qs and water chemistry should significantly affect the determination of representative elementary area and therefore need to be considered when predicting representative elementary area from spatial variability of low-order streams.