Population and community dynamics within ecosystems are driven by biological, chemical, and physical factors whose effects generally result from either external forcing: pressures originating from outside of the ecosystem boundaries (e.g., meteorological or anthropogenic in origin), or from internal self-organization: species interactions such as predation or competition. The aim of my research was to study the balance between these two general processes in plankton population dynamics and the relative impact of each in structuring aquatic pelagic communities. I performed this research in eight embayments along the southeastern shoreline of Lake Ontario that varied widely in water residence time (WRT) because of differences in basin volume, watershed area, and degree of lake connectivity, where WRT was taken as in indication of the extent of external forcing. I used three approaches in this research: (1) seasonal characterization of plankton dynamics and community characteristics in each embayment along the WRT gradient represented by the embayments; (2) an intensive assessment of one external force, upwelling-driven exchange flow, on two embayments with similar connectivity, but different in volume and watershed size; and (3) mesocosm experiments that analyzed the factors responsible for the resistance of the plankton community in one embayment to the establishment of newly introduced species. Overall, there was an underlying pattern of increasing internal self- organization with decreasing WRT, although the relationship was complicated by the physical and biological characteristics of the embayments that buffered them from external forcing. For external forcing to be effective, it had to be sufficiently strong to counterbalance the dilution effect of large embayment volume or the flow-restricting action of dense macrophyte stands. Plankton community composition also counteracted the expected effects of WRT, as characteristics such as high plankton rmax allowed populations to respond quickly enough to high flow that they were able to thrive and interact, muting the expected wash-out dynamics. Additional trophic levels (fish, macrophytes) inhibited the potential disturbance of resident community dynamics by invading species. Overall, while external forcing played an important role in these systems, it was not as dominant a force as expected, highlighting the strength of internal self-organization in structuring plankton community dynamics.