Prolonged events of anomalously warm sea water temperature, or marine heatwaves (MHWs), have major detrimental effects to marine ecosystems and the world’s economy. While frequency, duration and intensity of MHWs have been observed to increase in the global oceans, little is known about their potential occurrence and variability in estuarine systems due to limited data in these environments. In the present study we analyzed a novel data set with over three decades of continuous in situ temperature records to investigate MHWs in the largest and most productive estuary in the US: the Chesapeake Bay. MHWs occurred on average twice per year and lasted 11 days, resulting in 22 MHW days per year in the bay. Average intensities of MHWs were 3°C, with maximum peaks varying between 6 and 8°C, and yearly cumulative intensities of 72°C × days on average. Large co-occurrence of MHW events was observed between different regions of the bay (50–65%), and also between Chesapeake Bay and the Mid-Atlantic Bight (40–50%). These large co-occurrences, with relatively short lags (2–5 days), suggest that coherent large-scale air-sea heat flux is the dominant driver of MHWs in this region. MHWs were also linked to large-scale climate modes of variability: enhancement of MHW days in the Upper Bay were associated with the positive phase of Niño 1+2, while enhancement and suppression of MHW days in both the Mid and Lower Bay were associated with positive and negative phases of North Atlantic Oscillation, respectively. Finally, as a result of long-term warming of the Chesapeake Bay, significant trends were detected for MHW frequency, MHW days and yearly cumulative intensity. If these trends persist, by the end of the century the Chesapeake Bay will reach a semi-permanent MHW state, when extreme temperatures will be present over half of the year, and thus could have devastating impacts to the bay ecosystem, exacerbating eutrophication, increasing the severity of hypoxic events, killing benthic communities, causing shifts in species composition and decline in important commercial fishery species. Improving our basic understanding of MHWs in estuarine regions is necessary for their future predictability and to guide management decisions in these valuable environments.