We used a range of methods including tag and recapture, fyke nets, electrofishing and radio-tracking to investigate mesoscale movement of small to medium sized native fish in the highly regulated Macintyre and less-regulated Condamine Rivers of the Murray-Darling Basin. We define Mesoscale movement as being beyond a reach (riffle- pool complex) and may extend from hundreds of metres to tens of kilometres. We recorded meso-scale longitudinal movement by Hypseleotris spp., Neosilurus hyrtlii, Nematalosa erebi, Melanotaenia fluviatilis and Leiopotherapon unicolor associated with season, natural flow and flow stage. Flow stage also influenced direction of movement with aggregations of various species occurring below barriers during local flow events. We observed significantly lower catches during irrigation releases suggesting that movement cues are missing from artificial flow events. The worst drought on record has hampered efforts to study lateral movement. However, we did observe selective movement by Ambassis agassizii and Leiopotherapon unicolor to a small lagoon off the Macintyre River in summer. Subsequent sampling in this location suggested that spawning and recruitment had occurred post-connection. We discuss our findings in relation to loss of connectivity between habitats on the floodplain and within the river for small to medium sized fishes.