Estuaries feature diverse ecosystems with great biological production and favourable resources and landscapes for ecotourism. Increasing natural disasters have threatened the lives and safety of over 70% of the region's population in recent years. Rapid urbanisation and tourism have changed land use. This changes ecosystem structure and function, impacting service provision. This study developed a Bayesian Belief Network (BBN) model to assess the imbalance between socio-economic development and resource conservation using an ecosystem services (ES) approach. The BBN model helps synthesise and exchange information, provide decision-making data, evaluate trade-off possibilities and anticipate future situations when assessing ES. The BBN network model probabilistically evaluates ecosystem services using expertise, statistical modelling, geographic information systems and interviews. We assessed the comprehensive value of 17 forms of ES for four ecosystem groups over a period of 30 years. As a result, the cultural ecosystem services of some estuarial regions in Vietnam have the highest value and are showing an increasing trend, while the regulating ecosystem services are continuously fluctuating and decreasing. Provisioning ecosystem services are stable with small changes. This study also examined ES values in six landscape categories and created two ES change scenarios. The findings can help managers choose land-use and resource exploitation policies, understand the value of ecosystem services at the regional level and develop estuary sustainability strategies for long-term ecosystem service balance.