Many studies in ocean engineering and related fields need physical wave modelling in controlled environments. Monitoring the free surface elevation over time is essential to forming accurate waves. Various wave height measurement instruments can be used to determine the free surface elevation. However, measurements based on only one principle might lead to uncertain results. This study aims to compare measurements taken with capacitance-type and ultrasonic-type wave height gauges for the same wave models and analyze uncertainty in wave modelling. Nine different wave cases were tested using three-wave heights and three-wave frequencies. In a two-dimensional wave flume, the amplitude and frequency of the waves were controlled with a mechanical wave generator. The Guide on the Expression of Uncertainty in Measurement (GUM) presented by the Joint Committee for Guides in Metrology (JCGM) was used following ITTC procedures and guidelines. The processes for acquiring data, selecting data intervals, estimating amplitude and frequency, and analyzing uncertainty are presented and discussed. The measurements by the ultrasonic-type wave height gauge required a different input stroke for the wave generator and had more uncertainties associated with the amplitude of the measured waves. The findings highlight that identifying differences in measurement principles is significant for wave modelling.