A well-designed monitoring program is critical for determining the extent of human impacts and the effectiveness of restoration activities in aquatic ecosystems. This project considers the Nymboida River, northern NSW, as a case study for developing a biological monitoring program. Water extraction from the Nymboida weir pool alters the flow regime to downstream habitats. Algal biofilms, which respond to local hydraulic conditions, are used in this project as biological indicators of response to the altered flow regime downstream of the weir. Longitudinal change on the Nymboida (the difference in biofilm assemblage attributes between upstream and downstream of the weir) was compared with longitudinal change on 'reference' rivers (rivers that do not have a weir and represent the desired condition for the Nymboida given current water and land-use constraints). This design allows us to determine if longitudinal change in biofilm on the Nymboida is greater than what we would generally find on equivalent rivers without a weir. The high variability in biofilm attributes (algal composition, biofilm mass, organic matter content and chlorophyll a at monitoring sites is assessed up-front in the design of the monitoring program so that optimum levels of sample replication can be determined. This will ensure that resources can be allocated efficiently while still providing enough information for managers to make informed decisions.