Often overlooked, zoosporic fungal parasites of phytoplankton (‘chytrids’) are present in aquatic systems worldwide. Although extensive studies in lakes give insight into potential impacts of chytrid epidemics on phytoplankton blooms and organic matter cycling, the ecological significance of chytrid infections of phytoplankton is still poorly understood in lotic systems. Here, we report the first observations of chytrid parasites attached to multiple diatom species in the lower Columbia River. We isolated a chytrid parasite of the dominant spring bloom diatom, Asterionella formosa, and sequenced DNA from several regions within the ribosomal RNA gene. We also investigated the specificity of the A. formosa chytrid to host and non-host diatoms with isolated cultures and found no cross infection at the species level. In the Columbia River, alterations in the hydrograph following the installation of hydroelectric dams may have opened a niche for chytrid parasites. Greater retention times may allow diatoms to bloom and provide a prolonged interaction period whereby chytrid parasites are able to infect hosts. Future research is needed to assess the seasonality and severity of chytrid infections on diatoms in the lower Columbia River and to evaluate the potential role of zoosporic fungi in influencing the food web structure and biogeochemical cycling in river systems.