While algal blooms are common in eutrophic lakes, blooms can also occur in tributaries that load nutrients into the lake. We sampled six sites along a 122-km stretch of the Maumee River May through October 2018 and 2019 at weekly to biweekly intervals to determine if algal blooms occur, in particular toxic cyanobacteria, and to provide insights on potential environmental drivers of blooms. Samples were analyzed for concentrations of potamoplankton (=riverine phytoplankton), chlorophyll a , nutrients, cyanobacterial toxins , microcystins and saxitoxins, and cyanotoxin genes ( mcyE and sxtA ). Extreme precipitation in 2019 resulted in more high discharge events during 2019 than in 2018. Chlorophyll a ranged from 50 µg/L to 300 µg/L during periods of low discharge (<50 m 3 /s), and green algae and diatoms accounted for the majority of the chlorophyll a . In both years, cyanobacteria comprised a low proportion of all chlorophyll a , usually<20 %, but microcystins and saxitoxins were detectable in 38.7 % and 16.7 % samples, respectively, and mcyE and sxtA were detected in 36.2 % and 59.7 % samples, respectively. Therefore, cyanotoxins were present even when cyanobacteria were not at bloom densities. Chlorophyll a , cyanotoxin genes, and microcystins negatively correlated with discharge rate measured on the date of sample collection. Together our results suggest that cyanotoxins can occur in any portion of the Maumee River during low discharge conditions. Climate change is expected to reduce precipitation during the warm summer months in the Maumee River watershed and thus possibly increase the frequency of low discharge conditions that favor cyanobacteria.