Harmful algal blooms caused by toxin‐producing species of the diatom genus Pseudo‐nitzschia have been linked to anomalously warm ocean conditions in the Northern California Current System. This study compares summertime concentrations of Pseudo‐nitzschia spp. and the toxin they produce, domoic acid, during a marine heatwave year (2019) and a climatologically neutral year (2021). An Imaging FlowCytobot was installed on a fishery survey vessel alongside environmental sensors to continuously sample phytoplankton and oceanographic parameters. This was paired with targeted manual sample collections for nutrients, chlorophyll, and domoic acid. Accumulations of Pseudo‐nitzschia spp. were associated with upwelling zones and established hotspot regions: the Juan de Fuca Eddy, Heceta Bank, and Trinidad Head. Overall, however, Pseudo‐nitzschia spp. and domoic acid concentrations were low during both summers and appear to have been limited by nitrate. Nutrient availability may therefore modulate the response of Pseudo‐nitzschia spp. to warm anomalies. Comparison of these results with 2015, another marine heatwave year but one that produced record concentrations of Pseudo‐nitzschia spp. and domoic acid, suggests that the timing of marine heatwave conditions in the nearshore relative to seasonal upwelling plays a key role in determining whether a Pseudo‐nitzschia spp. harmful algal bloom will occur.