The uncertainty in estimating the wave spectrum from the records of wave elevation by heave–pitch–roll buoys is studied, considering the effects of the estimation method and the spectral resolution adopted in the process. This investigation utilizes measurements from a wave buoy moored in deep water in the South Atlantic Ocean. First, the spectra are computed using the autocorrelation function and the direct Fourier method. Second, the spectral resolution is tested in terms of degrees of freedom. The degrees of freedom are varied, and the resulting spectra and integrated parameters are computed, showing significant variability. A simple and robust methodology for determining the wave spectrum is suggested, which involves calculating the average energy density in each frequency band. The results of this methodology reduce the variability of the estimated parameters, improving overall accuracy while preserving frequency resolution, which is crucial in complex sea states. Additionally, to demonstrate the feasibility of the implemented approach, the final spectrum is fitted using an empirical model ideal for that type of spectrum. Finally, the performance and the goodness of the fit process for the final averaged curve are checked by widely used statistical metrics, such as R2 = 0.97 and root mean square error = 0.49.