A Plankton ecosystem model was developed to investigate effects of hydrodynamic processes including advection and diffusion on size-structured phytoplankton dynamics in the mesohaline zone of the York River estuarine system, Virginia, USA. The model included 12 state variables representing the distribution of carbon and nutrients in the surface mixed layer. Groupings of autotrophs and heterotrophs were based on cell site and ecological hierarchy Forcing functions included incident radiation, temperature, wind stress, mean How and tide which includes advective transport and turbulent mixing. The ecosystem model was developed in FORTRAN using differential equations that were solved using the 4th order Runge-Kutta technique. The model showed that microphytoplankton blooms during winter-spring resulted from a combination of vertical advection and diffusion of phytoplankton cells rather than in-situ production in the lower York River estuary.