This work aims to supplement the realization and validation of a higher-order well-balanced unstructured finite volume (FV) scheme, that has been relatively recently presented, for numerically simulating weakly non-linear weakly dispersive water waves over varying bathymetries. We in- vestigate and develop solution strategies for the sparse linear system that appears during this FV discretisation of a set of extended Boussinesq-type equations on unstructured meshes. The resultant linear system of equations must be solved at each discrete time step as to recover the actual velocity field of the flow and advance in time. The system’s coefficient matrix is sparse, un-symmetric and often ill-conditioned. Its characteristics are affected by physical quantities of the problem to be solved, such as the undisturbed water depth and the mesh topology. To this end, we investigate the application of different well-known iterative techniques, with and without the usage of preconditioners and reordering, for the solution of this sparse linear system. The iiterative methods considered are the GMRES and the BiCGSTAB, three preconditioning techniques, including different ILU factorizations and two different reordering techniques are implemented and discussed. An optimal strategy, in terms of computational efficiency and robustness, is finally proposed which combines the use of the BiCGSTAB method with the ILUT preconditioner and the Reverse Cuthill–McKee reordering.