Proliferations of benthic cyanobacteria associated with the production of neurotoxic cyanotoxins known as anatoxins have been increasingly observed in rivers worldwide. However, controls on their anatoxin production are poorly understood, as previous studies have found weak relationships between anatoxin concentrations and environmental factors such as water quality. This suggests that perhaps biotic factors, such as species interactions among co-occurring taxa, may influence anatoxin production. In this study, we investigated how algal and microbial assemblages within benthic mats dominated by one of two cyanobacterial taxa associated with anatoxins, Microcoleus and Anabaena, varied through time and among rivers and with variation in anatoxin concentrations. From June to September in 2022, we collected Microcoleus and Anabaena mats biweekly from the South Fork Eel, Russian, and Salmon Rivers in northern California. We quantified the relative abundances of algal groups with microscopy and bacteria with 16s rRNA, and analyzed samples for anatoxin concentrations using LC-MS/MS. Both algal and bacterial assemblages associated with Microcoleus significantly differed among rivers while assemblages associated with Anabaena were similar among rivers. Microcoleus samples from the South Fork Eel River were associated with higher relative abundances of nitrogen-fixing diatoms (Epithemia) and cyanobacteria (e.g., Anabaena, Nostoc) and had a higher median bacterial diversity than that of Microcoleus from the Salmon River as quantified by the Shannon Diversity Index (5.7 vs. 4.9). Anabaena samples from all three rivers had high relative abundances of diatoms (including Epithemia), coccoid cyanobacteria, and other anatoxin-producing cyanobacteria (especially Geitlerinema) but had similar bacterial diversity among rivers (5.5-5.6). Preliminary results suggest that algal and bacterial assemblages associated with Microcoleus and Anabaena changed with increasing anatoxin concentrations within the South Fork Eel River where anatoxin concentrations reached a maximum of over 100 μg anatoxins g-1 organic matter, but not for Anabaena in the Russian River where anatoxin concentrations only reached up to 5 μg anatoxins g-1 organic matter. Future work will identify taxa responsible for composition differences and will incorporate theoretical functional groups of the bacterial assemblages as determined by PICRUSt2.