Bibliography: pages 163-183. / A generic, size-based simulation model is developed to investigate the dynamics of carbon and nitrogen flows in plankton communities. All parameters in the model are determined by body size using empirically-determined relationships calculated from published data. The model is robust with respect to most parameters and assumptions. Because the model is based on general ecological principles, it can be used to simulate microplankton community interactions in any planktonic ecosystem. Two coastal ecosystems from the southern Benguela region in South Africa are simulated; one typical of the relatively stable surface waters on the Agulhas Bank and one typical of upwelling plumes, usually found off the west coast of South Africa. Simulated communities compare well with field observations in terms of standing stocks and size composition, and simulation results indicate that the small-scale structure of the two ecosystems and the processes occurring within them are relatively well understood. Consequently, the dynamic functioning of the two systems is investigated at the ecosystem level, using the simulation results. Hypothetical carbon flow networks are constructed, and the average importance of different flow pathways at different times is assessed. In both ecosystems, the vast majority of carbon flows pass through short, efficient-transfer pathways, although longer pathways are potentially possible. Simulation analyses are extended from coastal to oceanic food webs, and the model results are consistent with the hypothesis that oceanic phytoplankton have rapid rates of primary production. At-sea sampling of a phytoplankton bloom is mimicked by "sampling" from simulation output, and interpretation of the data using standard techniques is compared with the model output. The dangers of extrapolating from snapshot measurements is highlighted, and the experiment emphasizes the importance of size-fractionated sampling of phytoplankton. A hypothetical pelagic food web is described, consisting of at least five different trophic pathways from phytoplankton to pelagic fish. It is suggested that coastal waters probably have all the different pathways, and the relative importance and efficiency of the different pathways will determine the total fish production in an ecosystem.