Port Phillip Bay is the main spawning area for the Victorian western stock of Snapper, Chrysophrys auratus. The dynamics of the western stock are primarily driven by the recruitment success of Snapper in Port Phillip Bay. Recruitment success for Snapper in the bay is determined in the early larval stage. In this study we used a model of plankton dynamics in the bay to show that production of preferred prey for larvae (copepods) was determined by flows and associated nutrient inputs, and the effects of these on phytoplankton composition. Years of high larval survival and recruitment success occurred when production of preferred prey was high, and coincided with the early summer spawning period of Snapper. These years were characterised by moderate flows and nutrient inputs leading up to the spawning period that led to phytoplankton composition favouring flagellates. Years of very low flows and nutrient inputs led to an overall lack of plankton productivity and correspondingly poor larval survival and recruitment. Equally, years of high flows and nutrient inputs also led to poor recruitment because conditions in the plankton favoured diatoms that are a poorer food source for copepods, reducing production of these preferred prey. Overall, inputs of nutrients to Port Phillip Bay have a strong influence on the dynamics of the west Victorian Snapper stock, and the management of environmental flows and associated nutrients to the bay may be key factor in the ongoing sustainability of the fishery.