A system of ten coupled ordinary differential equations was developed to investigate the time-dependent behavior of phytoplankton and copepod populations associated with frontal eddy and bottom intrusion upwelling features on the outer southeastern U.S. continental shelf. Model equations describe the interactions of nitrate, ammonium, two phytoplankton size fractions (>10 μm and <10 μm), five copepod categories that represent the developmental stages of a population, and a detrital pool. Formulations for the biological processes are based primarily upon data obtained from laboratory and field experiments for southeastern U.S. continental shelf plankton populations. Time series of nutrient and plankton distributions obtained from GABEX II provide verification of model results. The simulated time dependent distributions for bottom intrusions show a phytoplankton maximum occurring approximately eight days after the nitrate maximum, and the copepod biomass peaks within eight to nine days after the phytoplankton. Frontal eddy simulations show the same succession except that the short time scale of these events precludes the development of large copepod blooms. To obtain the correct relative abundance of the two phytoplankton size fractions in the bottom intrusion simulations it was necessary to increase the cell death rate of the small (<10 μm) cell size fraction relative to the large cells (.15 d–1 vs. .1 d–1). The additional loss from the small cells may represent a transfer to a zooplankton or microzooplankton grazer that is not included in the model. The depth-averaged (20 to 40 m) carbon production calculated from the bottom intrusion simulation was approximately 4 mgC m–2d–1 which agrees with production values measured for bottom intrusions. Model simulations indicate that temperature is a potentially important factor in determining the trophic structure in bottom intrusions. Also the role of frequency of nutrient input, fecal pellet remineralization and phytoplankton growth coefficient in determining the biological distributions in bottom intrusions were evaluated with the model.