Drift of stream insects is one of the most ubiquitous forms of downstream dispersal and thought to be a key factor influencing the persistence of local populations. Identifying the factors that limit drift dispersal between habitat patches is needed to understand the connectivity of insect populations along river channels. We determined whether insects drifting between riffle habitats (i.e. patches of suitable habitat) were impeded by natural, slow-moving pools (i.e. unsuitable habitat), limiting dispersal to the next downstream riffle, by estimating drift rates entering and exiting pools. We also investigated whether the frequency of drift dispersal between riffle habitats decreased with increasing pool size (length, width and depth), resulting from increasing areas of low or zero current velocity and/or distance between habitat patches. We found that for the majority of study taxa (7 of the 8 taxa), drift dispersal between riffles was significantly hindered by the intervening pool habitat, supporting our prediction that natural, large slow-moving pools impede the number of invertebrates drifting between riffle habitats. There were three taxa whose drift rates were significantly reduced by increasing pool depth or width—Offadens hickmani, Austrophlebioides spp. and Austrosimulium spp., and weak relationships (p <.10) were also found for Coloburiscoides munionga and Asmicridea edwardsii. Drift was not associated with pool length for any species, suggesting that hydraulic conditions within a pool limit drift dispersal and not the total distance between riffle habitat patches. Overall, our results suggest drift dispersal seems unlikely to be a major mechanism of long distance dispersal, for at least some common insects. These findings indicate that drift may play a more limited role in stream insect dispersal than is commonly considered and that flying adults may therefore have much greater influence on connectivity among populations.