A four-box model of planktonic nutrient cycling was coupled to a high-resolution hindcast circulation model of the Oregon-Washington coast to assess the role of the Columbia River plume in shaping regional-scale patterns of phytoplankton biomass and productivity. The ecosystem model tracks nitrogen in four phases: dissolved nutrients, phytoplankton biomass, zooplankton biomass, and detritus. Model parameters were chosen using biological observations and shipboard process studies from two cruises in 2004 and 2005 conducted as part of the River Influences on Shelf Ecosystems program. In particular, community growth and grazing rates from 26 microzooplankton dilution experiments were used, in conjunction with analytical equilibrium solutions to the model equations, to diagnose key model rate parameters. The result is a simple model that reproduces both stocks (of nutrients, phytoplankton, and zooplankton) and rates (of phytoplankton growth and microzooplankton grazing) simultaneously. Transient plume circulation processes are found to modulate the Washington-Oregon upwelling ecosystem in two ways. First, the presence of the plume shifts primary production to deeper water: under weak or variable upwelling winds, 20% less primary production is seen on the inner shelf, and 10–20% more is seen past the 100 m isobath. River effects are smaller when upwelling is strong and sustained. Second, increased retention in the along-coast direction (i.e., episodic interruption of equatorward transport) causes a net shift toward older communities and increased micrograzer impact on both the Oregon and Washington shelves from the midshelf seaward.