Increasing human demand on the world's water resources has led to the construction of dams and diversions that cause major alterations to natural flow regimes and threaten riverine ecosystems globally. Consequently, water resource management now recognises the need to establish the extent to which flow regimes can be altered while maintaining the integrity of the ecosystem. However, the ecological consequences of changing the physical regime are often difficult to predict and, therefore, a well-designed monitoring program, capable of detecting directional change in aquatic biota is critical for assessing human impacts and evaluating the effectiveness of restoration activities. Altered hydrology can affect biofilm assemblages by influencing two counteracting flow-related processes - mass-transfer leading to biomass accrual and shear stress leading to biomass loss. This study uses biofilm assemblages to investigate the biological condition of the regulated Nymboida River, south-eastern Australia, under current flow management practices and to design a monitoring program capable of detecting a change in this condition as flow management practices are altered in the future. The outcome of this study is a scientifically defensible monitoring program that provides meaningful outcomes in both an ecological and managerial context.