The hydrological quantities governing the generation of riverbed waves (formed spontaneously on the bottoms of rivers) have been elucidated through geomorphological methods, laboratory experiments, stability analyses, numerical analyses, and other research methods.Recently, numerical analysis was performed with a fine spatial resolution.However, numerical analysis cannot always describe the real phenomena because it is based on assumptions.Therefore, understanding the physical phenomena by measurements with the same resolution as the numerical analysis is necessary.Measurement data with high resolution enable the construction of a duplicate of the measurement target on a computer, called a “digital twin”.To construct a digital twin of the process of riverbed wave generation and development, the geometries of the water surface and the river bottom must be measured simultaneously.We developed and verified a measurement method for the construction of a digital twin during the generation and development of riverbed waves.The measurement system uses two cameras and a line laser to simultaneously measure the water surface and river bottom.Accurate refraction correction at the water surface is possible by acquiring the shape of the water surface, allowing the bottom shape to be determined by geometric processing.The method provides submillimeter-accurate measurements of the water surface and bottom with a spatial resolution of 0.95 cm longitudinally and 0.038 cm transversely in a 12 m $\times$ 0.45 m channel and takes only one minute per measurement.This method can provide measurement results that contribute to the understanding of the formation and development of riverbed waves.