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Marine heat waves (MHWs) have been associated with extensive harmful algal blooms (HABs) in the northeast Pacific Ocean, but the degree to which these large-scale oceanographic events are mirrored in nearshore environments has not been well established. We compared phytoplankton assemblages in the Lower Columbia River Estuary (LCRE) during two Pacific MHWs that took place in 2015 and 2019, with observations from 2017, a year with no MHW. These data were paired with environmental data from the summers of 2015–2019 to characterize differences in estuarine conditions during MHWs that promote phytoplankton assemblage transitions and identify HAB-conducive conditions. Bloom densities of HAB taxa, Pseudo-nitzschia spp. (4.16 × 106 cells L−1) and Gymnodinium catenatum (5.66 × 106 cells L−1), were noted in the estuary during 2015 and 2019, respectively, 2 years where Pacific MHWs occurred during the summer months. These blooms coincided with estuary temperatures that were 1–2 ℃ above and river discharge volumes 46–48% lower than decadal daily averages. We identified patterns in the densities of several algal taxa associated with MHW-mediated low discharge in the LCRE, such as declines in tychopelagic diatoms and increasing abundance of pelagic marine taxa. We conclude that low river discharge, through extension of saline habitat area and longer residence times, likely contributed to the development of the observed marine HABs in the estuary. MHWs and associated declines in discharge are projected to become more common in the Pacific Northwest with climate change, which may alter late summer phytoplankton assemblages in the LCRE. [ABSTRACT FROM AUTHOR]