In recent decades, there has been an apparent increase in the prevalence of toxic benthic cyanobacterial proliferations. This has resulted in around 100 dog deaths in New Zealand alone and also has serious human health implications. The increase in these blooms has been associated with low flows and increased nutrient levels. Flow management is a commonly proposed method for controlling cyanobacterial blooms. High flow levels can restrict benthic cyanobacterial growth, but maintaining high flows can be difficult. Inducing substrate movement with flushing flows offers a solution, but managers lack effective tools for setting flow limits. Development of effective hydrological limit setting tools requires a thorough understanding of the relationship between cyanobacteria and bed substrate stability. This paper presents results from a study of cyanobacterial communities in the Canterbury Region, New Zealand. Community variables are compared with bed stability levels assessed using a novel multivariate index.