This paper presents a study dealing with increasing the computational efficiency in modeling floodplain inundation using a two-dimensional diffusive wave equation. To this end, the domain decomposition technique was used. The resulting one-dimensional diffusion equations were approximated in space with the modified finite element scheme, whereas time integration was carried out using the implicit two-level scheme. The proposed algorithm of the solution minimizes the numerical errors and is unconditionally stable. Consequently, it is possible to perform computations with a significantly greater time step than in the case of the explicit scheme. An additional efficiency improvement was achieved using the symmetry of the tridiagonal matrix of the arising system of nonlinear equations, due to the application of the parallelization strategy. The computational experiments showed that the proposed parallel implementation of the implicit scheme is very effective, at about two orders of magnitude with regard to computational time, in comparison with the explicit one.