Wetlands play a critical role in managing water quality, yet their application in tropical and subtropical environments—particularly for nutrient processing such as nitrogen removal—remains underdeveloped. A key factor in understanding and modelling wetland performance is accurate estimation of bathymetry and volume, which influence water residence time and nutrient processing capacity. This study investigated three methods to estimate wetland bathymetry and volume in 15 systems across wet and dry tropical regions of the Great Barrier Reef (GBR) catchments: (1) digital elevation models (DEM), (2) a novel approach based on aquatic vegetation depth limitation using drone imagery, and (3) traditional boat-based depth surveys. Method 2 involved reviewing 58 aquatic plant species found in the region and extracting depth limitation data to classify vegetation into four depth zones, which were then used to estimate volume. The four model zones include: Zone 1 – open water (floating and submerged species); Zone 2 – submerged macrophytes (rooted, fully submerged species); Zone 3 – emergent macrophytes (species partially above water); and Zone 4 – riparian vegetation (including floodplain plants). Vegetation extent and composition are critical for wetland function, and understanding depth preferences of desirable versus invasive species (e.g., Hymenachne amplexicaulis) is essential for long-term management and maintenance. The comparison of methods showed that DEM-based and vegetation-based approaches had near 1:1 agreement, while boat surveys slightly overestimated volume (possibly a consequence of not being able to access all parts of wetlands due to overgrowth of water plants – a major limitation with this method). Volume estimates ranged from 4,655 ML to 217,412 ML across sites. In some cases, all three methods produced similar results, though discrepancies were noted in others. This work presents a consistent and efficient method to estimate wetland volume in data-limited tropical areas and supports development of a new modelling platform to simulate nutrient cycling in coastal wetlands. This platform, incorporating vegetation zones and bathymetric detail, will guide managers, NRM groups, and industry in wetland design and maintenance, contributing to improved water quality outcomes and protection of the GBR World Heritage Area.