Marine heatwaves (MHWs) are increasing in frequency and intensity globally and are among the greatest threats to marine ecosystems. However, limited studies have characterized subsurface MHWs, particularly in shallow waters. We utilized nearly two decades of full water-column (~ 10 m) observations from a unique automated profiler in central California to characterize, for the first time, the vertical structure of MHWs in a shallow nearshore upwelling system. We found MHWs have similar average durations and intensities across all depths, but there were ~ 17% more bottom MHW days than surface MHW days. Nearly one third of bottom MHWs occurred independently of surface MHWs, indicating that satellites miss a significant fraction of events. MHWs showed distinct seasonality with more frequent and intense events during the fall/winter when weak stratification allowed for MHWs to occupy a larger portion of the water column and persist longer. During summer, strong stratification limited the vertical extent of MHWs, leading to surface- and bottom-trapped events with shorter durations and intensities. Additionally, MHW initiation and termination across depths was consistently linked to anomalously low and high coastal upwelling, respectively. This study highlights the need for expansion of subsurface monitoring of MHWs globally amid a warming planet.