This was the first study to analyze phytoplankton and zooplankton community size structure during hurricane passage. A three‐dimensional biophysical model was used to assess ecosystem dynamics, plankton biomass, and plankton distribution in the Gulf of Mexico during Hurricane Katrina (2005). Model simulations revealed that large phytoplankton were most responsive to hurricane‐induced turbulent mixing and nutrient injection, with increases in biomass along the hurricane track. Small phytoplankton, microzooplankton, and mesozooplankton biomass primarily shifted in location and increased in spatial extent as a result of Hurricane Katrina. Hurricane passage disrupted the distribution of plankton biomass associated with mesoscale eddies. Biomass minimums and maximums that resided in the center of warm‐ and cold‐core eddies and along eddy peripheries prior to hurricane passage were displaced during Hurricane Katrina.