Most communities are structured not by a single process but by some combination of top–down, bottom–up and supply‐side (i.e. juvenile recruitment) factors. However, establishing how multiple processes interact remains a fundamental challenge. For example, the recruitment, growth, and mortality of estuarine species can vary along the steep and numerous environmental and biological gradients typical of these habitats, but the relative importance of those gradients is generally unknown. We took a novel approach to this question by coupling long‐term field observations of the Olympia oyster Ostrea lurida in a central California estuary with a state‐space integral projection model. This approach revealed that the most parsimonious description of oyster population dynamics involved spatial variation in growth and adult mortality – but not juvenile mortality – as well as spatiotemporal variation in recruitment. These patterns match the available short‐term estimates of each of those processes from field studies, and reveal a synthetic view of oyster population dynamics. Larval recruitment has an interannual ‘boom and bust’ pattern, and during good recruitment years most larvae settle in the inner bay where water residence time is highest. Adult oyster mortality is also highest in the inner bay, where several invasive predators are abundant and lowest in the mid‐bay, where oyster growth is greatest (due to bottom–up factors), likely leading to a size refuge from native predators. Surprisingly, juvenile mortality was constant across the bay, possibly because of a lack of size refuge from native and invasive predators. Our research approach represents an important advance in disentangling the contributions of spatio–temporal variation in top–down, bottom–up and supply‐side forces to the dynamics of populations with open recruitment.