The principle that biological diversity stabilises ecosystem processes is central to ecology and conservation, with portfolio effects offering a useful framework to understand this dynamic. Borrowed from finance, portfolio effects suggest that diverse, asynchronous components such as species, subpopulations, or behaviours can buffer against environmental variability and enhance system stability. Here we treat individual estuary subpopulations as assets within a broader metapopulation portfolio, where asynchronous dynamics among and within estuaries reduce the risk of collapse and synchrony amplifies vulnerability. We analyse over 80 years of commercial catch data (1940–2023) from multiple estuaries along the New South Wales coast for more than 20 fish (e.g. mulloway, black bream, flathead) and crustacean species (e.g. blue swimmer crab, king prawns). We first quantify portfolio effects and spatial synchrony, to then examine how environmental drivers influence these patterns. Our results reveal variation in portfolio effects and differences in spatial synchrony patterns among species with increased estuarine and marine affinity. By quantifying portfolio effects and asynchrony, our analysis provides insights into the role of spatial dynamics and the stability of estuarine fish metapopulations. Doing so provides a novel lens to conserving biological complexity and catch diversification as strategies to foster resilience under increasing climate uncertainty.