Microfaunal samples were collected from within the channels of three rivers in north eastern Victoria, Australia (the Murray, Ovens and Broken Rivers) as a component of a study examining the effects of flow on the biota of lowland rivers in Australia. Samples were collected from the water column of the river channel and slackwaters and from the layer of water immediately above the bottom sediment of the slackwaters. There was no connectivity between the river channel and the floodplain wetlands for all three rivers during the sampling period. Substantial numbers of microfauna were resident in the slackwaters of all three rivers, with the greatest densities occurring close to the bottom sediment, with densities often exceeding 1000 animals l−1 whereas in the plankton samples densities were usually less than 500 animals l−1. The presence of large and diverse microfaunal communities and the lack of connectivity between the river channel and associated floodplain wetland indicate that these communities are capable of persisting and recruiting within riverine channel slackwaters.