Ocean color measurements from aircraft revealed an unusually strong fall bloom of phytoplankton in Chesapeake Bay after passage of Hurricane Isabel in September 2003. Flights conducted before (11 September) and after (24 September) Isabel showed a two-fold increase of chlorophyll-a (Chla) covering ~3000 km2 of the mid- to lower Bay, with an abrupt return to long-term average (LTA) Chla by early October. Wind mixing induced rapid de-stratification of the water column, injecting nitrogen (N) into the euphotic layer that supported a fall bloom of diatoms. Here we quantify a significant perturbation of the annual phytoplankton cycle in Chesapeake Bay, driven by Hurricane Isabel.