In wave flumes or basins, when simulating sea waves in physical models with reflective structures, there frequently arrive, on the wave maker paddle, important reflected waves, due to the structure, which affect the incident waves. So that the waves generated by the paddle movement are not perturbed, the paddle movement must be compensated in order that the reflected waves be absorbed and have no effect For this, the incident and the reflected spectra have to be separated. There exist several methods for separating incident and reflected spectra both in the time and the frequency domain. The methods considered in this paper belong to the last group. Basically, these methods consist in deducing the incident and reflected wave spectra from the observed wave spectra at two or more points located along a line parallel to the wave propagation direction. Besides separating the spectra, the model is also able to produce numerically simulated data with given characteristics of wave spectra and physical constraints. It can also be tested by both numerically simulated data and real data recorded by the different wave gages operating in the wave flume. Comparing the so-called two-gage method and the N-gage method in terms of the ability to reconstruct the incident and reflected wave spectra, and according to the numerical and physical tests already carried out, the N-gage method seems to produce more rigorous results than the two-gage method. For the work presented in this paper these two methods were implemented in computer for a bi-dimensional flume and numerical simulation procedures able to verify the methods were established. The results of the numerical simulations developed to test these two methods proved both methods to be quite accurate. The two methods were then applied to physical flume waves with satisfactory results. From the work reported in this paper a first version of a software package able to address the problem of unwanted wave reflection in wave flumes was developed. Transactions on the Built Environment vol 27, © 1997 WIT Press, www.witpress.com, ISSN 1743-3509