This paper develops a new implementation coupling optimisation-based anisotropic mesh adaptivity algorithms to a moving mesh numerical scour model, considering both turbulent suspended and bedload sediment transport. The significant flexibility over mesh structure and resolution, in space and time, that the coupling of these approaches provides makes this framework highly suitable for resolving individual marine structure scales with larger scale ocean dynamics. The use of mesh optimisation addresses the issue of poor mesh quality and/or inappropriate resolution that have compromised existing modelling approaches that apply mesh movement strategies alone, especially in the case of extreme scour. Discontinuous Galerkin finite element-based discretisation methods and a Reynolds Averaged Navier–Stokes-based turbulent modelling approach are used for the hydrodynamic fluid flow. In this work the model is verified in two dimensions for current-dominated scour near a horizontal pipeline. Combined adaptive mesh movement and anisotropic mesh optimisation is found to maintain both the quality and validity of the mesh in response to morphological bed evolution changes, even in the case where it is severely constrained by nearby structures.