Before regulation flows in the lower Murray were highly variable, as for most rivers in semi-arid regions. Major floods promoted large-scale recruitment of flora and fauna in riverine and floodplain communities, and seasonal floods maintained lower levels of recruitment. The regime changed with the construction of 10 low-level weirs in 1922–35, supplemented by the effects of dams in upstream areas. Flows remain variable but are much reduced in volume (about 44%). Low flows (100–300 Gl per month) have decreased five-fold and moderate flows (500–1500 Gl per month) have increased two-fold. Although the magnitude of peak seasonal flows has been diminished, the timing of flows is unaffected. The effects differ in the Valley and Gorge sections of the river, depending on local development of the floodplain and associated wetlands. The weirs have flooded once-temporary wetlands and contributed to problems of salinization. Weir operations cause daily stage fluctuations that diminish downstream, and the channel is developing a stepped gradient as a consequence of active deposition and erosion. Regulation has limited exchanges between the river and its floodplain, changed the nature of the littoral zone and generally created an environment inimical to many native species, notably fish. The key to rehabilitation may be to restore a more natural balance of low and medium flows, but this may be unrealistic given the needs of irrigators and other water users. Despite its evolutionary history of wide spatial and temporal variation, the Murray river-floodplain ecosystem evidently cannot accommodate these forms of disturbance.