A study was conducted to assess the impact of aquaculture activities on the ecosystem functions in Setiu Wetland, Malaysia. This study develops an ecosystem impact model based on formal (mathematical) relationships between aquaculture activities and Setiu Wetlands ecosystems using Bayesian Belief Network (BBN) approach. To represent different levels and kinds of aquaculture activity three policy options were used - status quo, a more intensive aquaculture production, conservation and ecotourism. The model integrates information gathered from experts and stakeholders. The results revealed that the impact of fish cage culture are likely differ under different management scenarios. The Conservation scenario was identified as the most attractive, followed by Ecotourism and the Status quo. The Intensive Aquaculture was the least desirable, with water column enrichment identified as the variable which is most vulnerable to the different aquaculture conditions. The BBN has indicated that the water column enrichment processes have the greatest effect on the model. Therefore formulating particular policies with regard to aquaculture management in Setiu Wetland would be sensible. Implication of the results is useful for the main stakeholders especially the policy makers in efforts towards managing the natural resources in a sustainable manner.