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It is widely assumed that phytoplankton abundance and productivity decline during temperate winters because of low irradiance and temperatures. However, winter phytoplankton blooms commonly occur in temperate estuaries, but they are often undocumented because of reduced water quality monitoring in winter. The small body of in situ work that has been done on winter blooms suggests they can be of enormous consequence to ecosystems. However, because monitoring is often reduced or stopped altogether during winter, it is unclear how widespread these blooms are or how long they can last. We analyzed an over 30-year record of monthly phytoplankton monitoring samples along with ad hoc sampling throughout Chesapeake Bay to assess the distributions of two common winter bloom species, Heterocapsa rotundata and Heterocapsa steinii, and the environmental conditions associated with these blooms. The long-term monitoring data revealed that H. rotundata blooms occur within a narrow salinity range (7–12) and potentially have different triggers depending upon the nutrient status of waters affected. The ad hoc sampling confirmed the occurrence of H. steinii blooms in the lower Chesapeake Bay, despite the lack of evidence for them from monthly monitoring data. Together, our findings demonstrate that winter blooms routinely occur in numerous locations throughout Chesapeake Bay and can last up to a month. Our findings suggest that while winter blooms are a staple of the Bay’s annual phytoplankton community, there are major data gaps reporting their occurrence highlighting the need for more frequent monitoring to understand factors promoting these blooms and their consequences on ecosystem productivity.