Patterns of dispersal in riverine populations of Australian smelt (Retropinna semoni) were examined using otolith chemistry (Mg:Ca, Mn:Ca, Sr:Ca, Ba:Ca) and genetic markers (allozymes, mtDNA, microsatellite DNA). During a period of prolonged low flows, young-of-year smelt were collected from 13 streams within three catchments of the southern Murray-Darling Basin, Australia. Spatial differences in otolith core and edge chemical signatures and high levels of genetic assignment to sampling locations were observed, suggesting that most recruits were retained in natal areas after spawning. Following a subsequent period of hydrological connection, the same cohort was sampled as 1-year-olds. Maximum likelihood estimation using otolith core chemistry data from these fish suggested that retention in natal areas was highly variable between years and a similar, though less pronounced, pattern was evident in genetic assignments. Partitioning of genetic variation among catchments was not significant (FCT < 0.004) and probably reflects disequilibrium between migration and genetic drift due to an historical population expansion (~270 000 years ago). Taken together, otolith chemistry and genetic analyses suggest that contemporary dispersal of smelt within these catchments is relatively restricted and may be mediated by changes in hydrological connectivity.