Onboard guidance systems have emerged to improve the safety of fishing vessels providing the skipper with simplified stability information. In the last years, the authors have developed a stability monitoring system that automatically estimates the natural roll frequency of the vessel. Although the performance was acceptable, there were some specific situations where the influence of external excitations reduced the accuracy of the stability estimations. In this work, a methodology to automatically estimate the wave encounter frequency from ship motions is proposed. Then, this methodology is included in the stability monitoring system. Towing tank tests of a mid-sized stern trawler in different conditions have been used to analyse the improvements obtained with this approach.