Coastal managers continue to be confronted with making management decisions with few data available and insight of the outcomes. Practical tools that can be used to inform on the effects of different scenarios of changes are particularly important to assist decision-making. This study has applied a Bayesian Belief Network (BBN) to investigate the contrasting effects of Sea Level Rise (SLR) scenarios and a reduction in tidal inundation on a tropical tidal wetland mosaic including saltmarshes, mangroves, and intertidal mudflats. We investigated: 1) the habitability of the study site for tidal vegetation under different scenarios associated with changes in inundation; and 2) the probability that the ecological values of export of crab zoea and blue carbon be supported under the scenarios. The study highlights that, without the ability to adjust to future SLR scenarios, saltmarshes here are likely to be lost to mangroves, and open water, under a scenario of 0.8 m SLR. Tidal inundation reduction decreased mangrove cover but increased habitability for terrestrial vegetation and subtidal herbaceous saltmarshes. SLR is likely to positively affect the blue carbon value but decreases the likelihood of the site holding high crab zoeae export values in saltmarsh areas. In contrast, a reduction of tidal inundation declined the likelihood of the site holding both high blue carbon and crab zoeae export values. The findings highlight the importance of "whole-of-system" approach to assessing the effects of different scenario changes in tidal inundation. Focusing only on one tidal wetland habitat and a single targeted value may affect the structure and functions of other habitat components of the coastal ecosystem mosaic. BBNs are useful tools to summarise preliminary assessments of the potential effects of tidal inundation changes on wetland ecosystems, which may assist managers to make the most informed decision to conserve and restore coastal transitional areas.