Plankton dynamics in large rivers are shaped by strong hydrologic regulation and pronounced seasonal variability, yet long-term patterns remain unclear. We examined phytoplankton and zooplankton abundance from 2009 to 2021 across 13 mainstem and 4 tributary sites in the Kootenai River basin. Analysis of the annual April-June data showed that phytoplankton communities were generally dominated by Bacillariophyta, while zooplankton assemblages across all sites were consistently dominated by Rotifera. However, during June 2019-2021, phytoplankton communities across the river network exhibited a pronounced shift away from diatom dominance toward increased contributions from microflagellates and picoplankton, coinciding with elevated zooplankton abundance. Further analysis of extended seasonal records in two mainstem sites (from early spring through late summer) revealed that phytoplankton abundance exhibited consistent spring-early summer peaks while zooplankton’s abundance displayed a delayed response compared to phytoplankton, suggesting bottom-up control during the early growing season. Moreover, several mainstem sites exhibited recurrent periods of elevated cyanobacteria abundance during mid to late summer (June-September). In contrast, tributary sites displayed more episodic and short-lived cyanobacteria increases, with sharp peaks occurring in some years where cyanobacteria temporarily equaled or exceeded Bacillariophyta abundance. Relationships between zooplankton abundance and environmental drivers were seasonally variable, with temperature effects strongest in spring and discharge dominating in summer. This multi-year analysis advances understanding of phytoplankton and zooplankton dynamics at the base of the food web, with direct relevance for adaptive management decisions to support higher trophic levels in oligotrophic river systems.