We used a biophysical model to examine the impacts of the 2014–2017 Northeast Pacific Marine Heatwave on plankton in the Salish Sea. Warming was strongest in the Juan de Fuca Strait, increasing phytoplankton growth. The Strait of Georgia showed stronger links to the North Pacific Gyre Oscillation with warming beyond 2017 and a reduction in large phytoplankton. Results highlight that multiple marine heatwaves can overlap within one waterbody, each with distinct effects on the local food web.