Accuracy and mesh generation are key issues for the high-resolution hydrodynamic modelling of the whole Great Barrier Reef. Our objective is to generate suitable unstructured grids that can resolve topological and dynamical features like tidal jets and recirculation eddies in the wake of islands. A new strategy is suggested to refine the mesh in areas of interest taking into account the bathymetric field and an approximated distance to islands and reefs. Such a distance is obtained by solving an elliptic differential operator, with specific boundary conditions. Meshes produced illustrate both the validity and the efficiency of the adaptive strategy. Selection of refinement and geometrical parameters is discussed.