Reservoirs and downstream rivers draining Oregon’s Cascade Range provide critical water supplies for over 1.5 million residents in dozens of communities. These waters also support planktonic and benthic cyanobacteria that produce cyanotoxins that may degrade water quality for drinking, recreation, aquatic life, and other beneficial uses. This 2016–2020 survey examined the sources and transport of four cyanotoxins—microcystins, cylindrospermopsins, anatoxins, and saxitoxins—in six river systems feeding 18 drinking water treatment plants (DWTPs) in northwestern Oregon. Benthic cyanobacteria, plankton net tows, and (or) Solid-Phase Adsorption Toxin Tracking (SPATT) samples were collected from 65 sites, including tributaries, reservoirs, main stems, and sites at or upstream from DWTPs. Concentrated extracts (320 samples) were analyzed with enzyme-linked immuno-sorbent assays (ELISA), resulting in >90% detection. Benthic cyanobacteria (n = 80) mostly Nostoc, Phormidium, Microcoleus, and Oscillatoria, yielded microcystins (76% detection), cylindrospermopsins (41%), anatoxins (45%), and saxitoxins (39%). Plankton net tow samples from tributaries and main stems (n = 94) contained saxitoxins (84%), microcystins (77%), anatoxins (25%), and cylindrospermopsins (22%), revealing their transport in seston. SPATT sampler extracts (n = 146) yielded anatoxins (81%), microcystins (66%), saxitoxins (37%), and cylindrospermopsins (32%), indicating their presence dissolved in the water. Reservoir plankton net tow samples (n = 15), most often containing Dolichospermum, yielded microcystins (87%), cylindrospermopsins (73%), and anatoxins (47%), but no saxitoxins. The high detection frequencies of cyanotoxins at sites upstream from DWTP intakes, and at sites popular for recreation, where salmon and steelhead continue to exist, highlight the need for additional study on these cyanobacteria and the factors that promote production of cyanotoxins to minimize effects on humans, aquatic ecosystems, and economies.