The flow regime of the Wimmera River was substantially modified due to the construction of a water supply reservoir. Samples of diatoms, soft algae and measurements of water quality were analysed at ten sampling sites for three years (between February 2012 and November 2014) along the MacKenzie River, a tributary of the Wimmera River, in different seasons and under different flow regimes, to understand the spatial and temporal variation in the relationship between algal communities, water quality and stream condition. Baseline information on algal communities and water quality was collected during base flow conditions, while experiments on the effect of water releases on algal communities were based on flow regime variations (manipulated flow regimes), specifically on the algae community structure, water quality and ecosystem function. Algal species composition changed along the river under different flow regimes and different seasons. Under base flow, Bacillariophyta (diatoms) were more abundant upstream and filamentous green algae were more abundant downstream.The results showed that the algal composition shifted downstream after water release events. Chlorophyta (Green algae), Cyanophyta (Blue-green algae) and Chrysophyta gradually increased from upstream to downstream under base flow conditions, and before water releases, whereas diatoms were greater upstream and increased downstream after water releases. The results suggest that by tailoring the discharge and duration of the river flows, through the amalgamation of consumptive and environmental flows would improve the condition of the stream, and supplementing the positive effects of the flows dedicated to improving environmental outcomes.