Intermittent stream channels are often used as a conduit of water for agricultural use. This alters critical aspects of the natural flow regime including the volume, variability and seasonality, while the open channel and drain networks experience high evaporative losses. As part of an agreement to increase water-use efficiency in Australia’s largest river basin (the Murray- Darling), a major water-saving pipeline has been constructed to replace the Broken-Boosey Creek system as the primary means of delivering water supplies to several small townships in northern Victoria. Consequently, several streams, which for the past 100 years have received highly regulated perennial flows, are being reverted back to a natural, intermittent flow regime, with low and cease-to-flow periods occurring throughout the summer months. This large-scale flow restoration has provided the opportunity to examine the relationship between hydrology, physical habitat and fish assemblages. The collection of pre-restoration data from a number of sites along a hydrological gradient has provided clear predictions about what changes to expect once flows are altered – namely that large bodied fish will be replaced by an assemblage of small bodied native and exotic species capable of tolerating extremes in environmental conditions. These predictions and their underlying mechanisms are now being evaluated. This research represents one of the first studies to examine ecological responses to a large-scale flow regime restoration project undertaken in Australia.