Biotas are adapted to historical patterns of flow variability in river systems and contemporary local assemblage composition will be shaped by the prevailing flow regime. Extremes of the low-flow regime are major ecological perturbations and can significantly influence stream assemblages by the loss of flowing water and total aquatic habitat, deterioration of water quality and alteration of food resources. Using data from historical biomonitoring programs, we determined whether invertebrate assemblages that had been exposed to severe flow reduction or cessation during the previous 12 months were dominated by taxa tolerant of low dissolved-oxygen concentrations, low water velocities and high temperatures. We estimated hydroaerophily, rheophily and thermophily of each invertebrate family based on its occurrence and associated environmental measurements for 3139 samples collected in New South Wales, Australia, in 2004–2012. Boosted regression tree modelling was used to test the response of assemblage trait composition to antecedent flows using a subset of samples from riffle (n=38) and pool-edge (n=159) habitats near hydrological gauges. Catchment land use and long-term measures of climate were also included as model predictors. Antecedent low flows were significantly associated with lower rheophily and aerophily and higher thermophily in riffle assemblages (73%, 64% and 74% relative importance respectively). For pool-edge assemblages, antecedent low flows were more weakly associated with rheophily and thermophily (20% and 11 % influence), but strongly associated with hydroaerophily (50% influence). The strong low flow-trait relationships for the riffle fauna suggest that any increase in the severity and duration of low flows because of water abstraction or climate change will impact on fauna in fast-flowing habitats. Pool-edge assemblages are probably adapted to frequent exposure to low velocity and warm temperatures and thus less influenced by low flows. However, invertebrates intolerant of low dissolved-oxygen levels appear to be at risk from increases in low flows.