Lowland rivers impounded by weirs are often operated to provide stable water levels. In the lower River Murray, stable water levels promote algal biofilms dominated by stalked diatoms, filamentous green algae and Cyanobacteria. In summer 2005–2006, the Lock 5 weir pool was surcharged for environmental benefit. Algal biofilms grown on artificial substrates were compared to the following year when the water level remained stable. On both occasions, substrates were fixed at 300-mm depth in the river channel and a connected wetland. During the surcharge, additional floating substrates were deployed to control for the change in water level. The algal communities that developed during both years were dominated by diatoms. A greater diversity in the biofilm community was evident during the 4-month surcharge when compared with the following year. This was due to a much greater change in algal biofilm community composition over the 4 months of the surcharge, compared with biofilms grown during a period of stable water level, when the community changed little after 1 month. The lack of difference between fixed and floating substrates suggests that the change in water level was not responsible for the difference between the surcharge and stable level biofilms. Possible reasons for the difference between years include light, nutrients and water temperature. Although the effect of the surcharge could not be definitively defined, these results provide some evidence that weir pool surcharge may be used to improve algal biofilm diversity when compared with the current stable water level regime. Copyright © 2011 John Wiley & Sons, Ltd.