Proliferations of riverine benthic cyanobacteria and associated toxins have increasingly become a public health concern around the globe; however, little is known about benthic cyanobacteria compared to planktonic cyanobacteria. To further understand environmental controls on the timing of benthic cyanobacteria growth and toxin production, we collected biweekly samples of benthic Microcoleus and Anabaena mats for community composition and anatoxin-a (ATX) concentrations and surface water samples from June to September 2022 in the South Fork Eel, Russian, and Salmon Rivers of northern California, USA. Additionally, we collected continuous discharge, temperature, and dissolved oxygen data from high-frequency sensors to estimate daily metabolism in each river. ATX concentrations ranged from 0 to 11,219 μg/L of mat material for Microcoleus and 0 to 2,912.4 μg/L of mat material for Anabaena. Highest ATX concentrations were found in the South Fork Eel River ranging from 0 to 11,219 μg/L with a median of 41.61 μg/L of mat material. Lowest ATX concentrations were found in the Salmon River ranging from 0 to 2.74 μg/L, though sampling was interrupted mid-sampling by wildfires possibly preventing sampling at the time of peak anatoxin production. ATX concentrations in the South Fork Eel peaked mid-sampling during early August, while ATX concentrations did not increase until September in the Russian River. ATX concentrations were temporally autocorrelated within each river, but there were no strong correlations between water nutrient concentrations, temperature, flow and mat ATX concentrations. Further work will explore the degree of synchrony among ATX concentrations, variation of benthic community composition, and river ecosystem productivity. Investigating how environmental conditions modify the relationship between cyanobacterial growth and cyanotoxin production and the degree of synchrony with river productivity dynamics should improve our ability to predict the timing and magnitude of cyanotoxin production in rivers.