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Dams, increasingly common in riverine systems worldwide, are particularly prevalent on the Columbia River (CR) in the United States. Hydroelectric projects, including both storage and run-of-river (i.e., minimal storage) structures, on the mainstem CR highly manage water flow, often by releasing water over (rather than through) dams as "spill." To test the effects of run-of-river dam spill on microplankton abundance and composition, we sampled above and below two dams in the lower CR before and during spill conditions in spring 2016 and during and after spill conditions in late summer 2007. We tested the effects of location (i.e., above vs. below dams), spill condition (i.e., before, during, and after spill), and their interaction on microplankton abundance. Generally, diatoms were most abundant during springtime, whereas cyanobacteria were most abundant in late summer. Most taxa were not significantly different in abundance above and below dams, regardless of spill status; although cyanobacteria abundance was marginally higher below dams in summer 2007 (p = .04). Abundances of all taxa were significantly different between pre-spill and spill periods in spring 2016, whereas only diatom and flagellate abundances were significantly different between spill and post-spill periods in summer 2007. We conclude that spill conditions may influence microplankton abundance, but are not likely to affect microplankton communities on either side of run-of-river dams on the CR. This is important information for dam managers concerned about ecosystem impacts of spill.