Global demand for freshwater has led to unprecedented levels of water abstraction from riverine systems. This has resulted in large alterations in natural river flows. The deleterious impacts of reduced flows on fish and macroinvertebrate abundances have been thoroughly investigated; in contrast, there is a limited understanding of the potential for changes in the abundance of nuisance benthic algal/cyanobacterial blooms. In New Zealand, Phormidium sp. blooms are common in numerous rivers during summer low flows. In this study, an in-stream habitat assessment is used to examine the relationship between Phormidium habitat availability and reducing flows. Over 650 observations of Phormidium mats, from seven sites (Hutt River, lower North Island, New Zealand), were used to construct habitat suitability curves for depth, velocity and substrate. Preference curves were fitted using both the ‘forage ratio’ and ‘quantile regression’ methods. Phormidium growth, observed at all seven sites, increased significantly from upstream (uppermost site, 5.2% mat cover) to downstream (63.5%). The habitat suitability curves revealed Phormidium had a large tolerance to velocity, depth and substrate type. Consequently, decreases in flow had only negligible effects on available Phormidium habitat. During periods of stable flow, Phormidium abundance positively correlated with increased nitrogen concentrations, potentially explaining the large variation in Phormidium cover from upstream to downstream. Quantile regression generated habitat suitability criteria were a more accurate predictor of available Phormidium habitat than the forage ratio criteria.