The dispersal of biota between populations is a key factor influencing the persistence of populations. In rivers, identifying constraints to drift dispersal between habitat patches is critical for greater understanding of the spatial extent of populations, recolonisation and river restoration. We determined whether stream insects drifting between riffle habitats (i.e. patches of suitable habitat) were impeded by pools (i.e. unsuitable habitat), limiting dispersal to the next downstream riffle. We measured invertebrate drift entering and exiting each of 13 pools, focusing on 13 species. We found that for 10 species, drift dispersal between riffles was significantly reduced by the intervening pool habitat, with the baetid, Offadens hickmani, showing the greatest reduction in drift numbers (60% reduction). The dispersal between riffle habitats for 9 species was related to one or more aspects of pool morphology. These relationships were consistent with the prediction that dispersal was increasingly impeded with greater areas of low or zero velocity within pools. Our results demonstrate that the drift of stream insects between habitat patches is limited by the intervening pool hydraulic conditions and individual species drift behaviours.