Observations of Alexandrium fundyense in the Gulf of Maine indicate several salient characteristics of the vegetative cell distributions: patterns of abundance are gulf-wide in geographic scope; their main features occur in association with the Maine Coastal Current; and the center of mass of the distribution shifts upstream from west to east during the growing season from April to August. The mechanisms underlying these aspects are investigated using coupled physical-biological simulations that represent the population dynamics of A. fundyense within the seasonal mean flow. A model that includes germination, growth, mortality, and nutrient limitation is qualitatively consistent with the observations. Germination from resting cysts appears to be a key aspect of the population dynamics that confines the cell distribution near the coastal margin, as simulations based on a uniform initial inoculum of vegetative cells across the Gulf of Maine produces blooms that are broader in geographic extent than is observed. In general, cells germinated from the major cyst beds (in the Bay of Fundy and near Penobscot and Casco Bays) are advected in the alongshore direction from east to west in the coastal current. Growth of the vegetative cells is limited primarily by temperature from April through June throughout the gulf, whereas nutrient limitation occurs in July and August in the western gulf. Thus the seasonal shift in the center of mass of cells from west to east can be explained by changing growth conditions: growth is more rapid in the western gulf early in the season due to warmer temperatures, whereas growth is more rapid in the eastern gulf later in the season due to severe nutrient limitation in the western gulf during that time period. A simple model of encystment based on nutrient limitation predicts deposition of new cysts in the vicinity of the observed cyst bed offshore of Casco and Penobscot Bays, suggesting a pathway of re-seeding the bed from cells advected downstream in the coastal current. A retentive gyre at the mouth of the Bay of Fundy tends to favor re-seeding that cyst bed from local populations.