Climate change and other anthropogenic pressures are impacting biodiversity and altering the structure, function, and stability of ecosystems worldwide. Understanding the drivers of coastal ecosystem stability under environmental change remains a global challenge. In this study, we investigated the temporal (>30-years) and spatial (region, estuary, and site) stability dynamics of estuarine macrobenthic metacommunities across New Zealand. Our study provides insights into the mechanisms underpinning community stability in estuarine ecosystems, including that metacommunity dynamics reduce species synchrony and thereby increase stability in heterogeneous estuarine ecosystems. Our findings revealed that species synchrony was the dominant driver of community stability across spatial scales and across estuaries over time rather that species richness or any other environmental variable. Overall, the inverse correlation between synchrony and stability demonstrated that compensatory dynamics are crucial to maintaining estuarine ecosystem functions and services.