Crown of Thorns Starfish outbreaks on the GBR are driven by the dispersal of COTS larvae by ocean currents. Robust estimates of dispersal are therefore important components of understanding COTS outbreaks on the GBR, and of effective control using manual culling. Biophysical modelling of dispersal remains extremely challenging, due to limited knowledge of their biology, and of the complex and varying current patterns in and around the GBR lagoon. Here, we compare COTS dispersal patterns estimated using three different hydrodynamic models of the GBR: (1) SLIM, a 2D and unstructured grid down to 250m, (2) eReefs, a 3D and 1km finite difference, and (3) GBRL, a 1.6km, 3D, finite difference model with additional reef parametrisation. We assess the strengths and limitations of the three models, compared against available observation of velocities and sea surface elevation across the domain. Results from the models’ assessments and the biology assumptions are used to produce a probabilistic description of COTS dispersal. This approach allows the evaluation of structural and parametric uncertainties of the dynamics of complex systems. Results are used to produce more robust estimates of COTS dispersal that can be used to support prioritisation of reefs for control.