Many harbor applications are based on the solution of linear elliptic agitation problems for many spectral conditions. One of the main goals consists in computing the linear combination of numerous simulations of the harbor agitation problem, using monochromatic waves of different spectral components (i.e. frequency and incoming wave direction). In practice, the standard strategy selects the number of wave components according to a prescribed discretization of the 2D input spectra. The main issue relies on some quantities of interest that are very sensitive to the level of refinement of the spectra, such as the significant wave height at every mesh point or the identification of resonance modes induced by long wave scattering. In many cases, achieving enough quality in these quantities may impose numerous simulations and, consequently, non-practical computer costs. This can drastically limit the final accuracy of results. To overcome this situation, here a new strategy is proposed to efficiently solve a large number of harbor agitation problems derived from dense discretizations of the 2D input spectra. The strategy is based on the combination of two different numerical approaches. Firstly, each required monochromatic simulation is solved via high order NURBS (non-uniform rational B-splines) enhanced finite elements (NEFEM). More precisely, NEFEM captures the exact harbor geometry using large mesh elements that produce accurate solutions and significant savings on the system size, particularly in long wave cases. Secondly, a model order reduction technique is used to approximate the original elliptic harbor model by a so-called surrogate model. The main advantage is that, once the surrogate model is constructed, it can be rapidly evaluated to provide simulations for any value of the spectral components within a range of interest, and without the need of solving any new harbor agitation problem (as the standard strategy does). Thus, this enables the possibility of using any desired discretization of the 2D input spectra with no additional computer cost. The construction of the surrogate model is performed using the proper generalized decomposition method with a novel incremental computation along the frequency dimension. The proposed strategy is discussed, and its superior performance with respect to standard strategies is demonstrated, on two harbor agitation examples with several applications.