Evaluating bed morphological structure and evolution (specifically the scoured bed level) accurately using numerical models is critical for analyses of the stability of many marine structures. This paper discusses the performance of an implementation within Fluidity, an open source, general purpose, computational fluid dynamics (CFD) code, capable of handling arbitrary multi-scale unstructured tetrahedral meshes and including algorithms to perform dynamic anisotropic mesh adaptivity. The flexibility over mesh structure and resolution that these capabilities provide makes it potentially highly suitable for coupling the structural scale with larger scale ocean dynamics. In this very preliminary study the solver approach is demonstrated for an idealised scenario. Discontinuous Galerkin finite-element (DG-FEM) based discretisation methods have been used for the hydrodynamics and morphological calculations, and automatic mesh deformation has been utilised to account for bed evolution changes while preserving the validity and quality of the mesh. In future work, the solver will be used in three-dimensional impinging jet and other industrial and environmental scour studies.