Pelagic ecosystems are inherently complex in coastal inlets where they are controlled by physical processes and influenced by biogeochemical and foodweb interactions. Meteorological events are important drivers of this ecological variability. This thesis investigates their effect on the plankton dynamics of Lunenburg Bay, an inlet on the Atlantic coast of Nova Scotia (Canada). In this region, meteorological events are dominated by upwelling in summer, which are a dominant source of flushing and nutrient variability for the inlets. Despite these events, which induce phytoplankton blooms in other regions, the concentration of phytoplankton as chlorophyll remains relatively low throughout the summer in Lunenburg Bay. To reveal the underlying processes limiting the development of phytoplankton biomass, and therefore to improve our understanding of the factors regulating plankton dynamics in this inlet, the objectives of this thesis are to determine the main drivers of variability in phytoplankton biomass and plankton community structure, and to identify the factors limiting the development of phytoplankton biomass in Lunenburg Bay. For that, I use a dataset collected at a coastal observatory located in Lunenburg Bay that covers the years 2003–2006, complemented by a series of transects carried out in summer 2006. The dataset covers physical, chemical and biological properties of the bay, including plankton taxonomy. Two types of physical-biological coupled models are developed: a low-resolution box model of Lunenburg Bay with steady-state wind forcing, and a high-resolution nested model of Lunenburg Bay using the Regional Ocean Modelling System (ROMS) to hindcast a series of upwelling events in 2006. The results reveal that four factors regulate the phytoplankton response to upwelling events in Lunenburg Bay, namely (1) the duration of an upwelling event, (2) the low nitrate concentration in source waters, (3) the flushing rate of the inlet (hence transport), and (4) the bathymetry along the inshore-offshore axis of the bay. In addition, (5) the occurrence of upwelling and (6) the inshore-offshore gradient of increasing depth influence the structure of respectively phytoplankton and zooplankton communities, indicating a dissimilarity in the processes structuring plankton communities in the lower food web. A conceptual model is then developed to describe the role of transport and nitrate concentration in source waters in controlling plankton dynamics in an inlet.