Freshwater mussels (Bivalvia: Unionoida) are an integral component of freshwater ecosystems. Historically, they were an important part of the diet and material culture of indigenous peoples, including until recently the Karuk Tribe of California. This study represents the first systematic survey of freshwater mussels in the Klamath River Basin of northwestern California, where little is known about mussel distribution, abundance, habitat associations, or conservation status. We snorkel surveyed 82 sites on the mid Klamath River and sections of nine major tributaries to assess abundance, distribution, and habitat use of mussels at three different spatial scales. We identified all three western North American mussel genera (Margaritifera, Gonidea, and Anodonta) in the Klamath River, with Gonidea abundant and widely distributed within the mainstem, and Anodonta and Margaritifera present in low numbers and restricted in distribution. At the landscape scale we observed a negative relationship between mussel abundance and measures of hydrological variability. At the mesohabitat scale, bank type, channel unit type, and their interaction were important predictors of mussel distribution. At the microhabitat scale, bank type, substrate type, and flow refuge presence were important predictors of mussel distribution. Together, our results suggest the common influence of hydraulics and substrate stability as drivers of mussel distribution in the Klamath, which agrees with the findings of other recent studies of mussel distribution. Our results also illuminate where habitat protection and restoration efforts should be directed within the mid Klamath subbasin to aid in mussel conservation.