Proliferations of the benthic anatoxin-producing cyanobacterium Phormidium are increasing in prevalence in cobble-bed rivers worldwide. This proliferation is of particular concern when rivers are used as sources of drinking water or for recreation. Little is known about the physicochemical variables promoting proliferations, and our existing knowledge is based on data from only a few rivers. We assessed Phormidium cover, physicochemical variables, and anatoxin concentrations at 10 sites in 7 New Zealand rivers every week for 2 y. Generalized additive mixed models (GAMMs) identified dissolved inorganic N (DIN) over the accrual period <0.8 mg/L, dissolved reactive P accrual <0.005 mg/L, water temperatures >15°C, and conductivity as having positive and statistically significant effects on % Phormidium cover. Flow intensity, expressed relative to the long-term median, had a positive effect up to 0.4× the median flow and a negative effect when >0.5× the median flow. Quantile regression models showed marked variability among sites in relation to the flow intensity required to reduce % Phormidium cover (90ᵗʰ percentile ranged 0.65–249× the long-term median flow). Anatoxins were detected in variable concentrations in samples from 7 of the 10 sites. GAMMs identified strong relationships between elevated toxin concentrations and low conductivity and increasing % Phormidium cover, and significantly lower toxin concentrations when DIN was <0.2 mg/L. These data demonstrate that multiple physicochemical variables influence Phormidium proliferations and toxin concentrations and indicate that the relative importance of these variables differs among rivers and sites.