1. With the aim of determining whether patterns of variation in macroinvertebrate assemblage composition across the hierarchy of spatial units in two lowland rivers changed during a supra-seasonal drought (1997–2000), patterns during a reduced flow season (1999–2000) were compared with those during two preceding higher flow seasons (1997–98 and 1998–99) using samples from the Glenelg and Wimmera Rivers, two lowland regulated rivers in western Victoria, Australia.
2. We hypothesised that (i) differences between reaches would increase during the reduced flow season owing to decreased hydrological connectivity, (ii) differences between the habitats would decrease because the cessation of flow in run habitats should cause them to become more similar to pool habitats and (iii) differences between microhabitats would also decrease because of reduced scour of inorganic substrata and large woody debris.
3. During each season, macroinvertebrates were sampled from three microhabitats (sand/silt substratum, large woody debris and macrophytes) that were hierarchically nested within a run or pool habitat and within one of three reaches within each river. A range of physico-chemical variables was also sampled.
4. Analysis of similarity showed that assemblage composition in both rivers during the higher flow seasons differed more among microhabitats than other spatial units. However, during the reduced flow season, assemblage composition in the Wimmera River differed most among reaches. This change in pattern was associated with the combined effects of decreased flow and longitudinal increases in salinity. In contrast, the fauna of the Glenelg River appeared to be resistant to the effects of the reduced flow season, owing to limited decline in water quality despite lower river discharge.
5. As salinisation and poor water quality in the Wimmera River result from human activities in the catchment, these results support the idea that human impacts on rivers can change macroinvertebrate scaling patterns and exacerbate the effects of drought beyond the tolerance of many riverine macroinvertebrates.