The frequency of droughts and floods is increasing due to the extreme climate. Proper water resource planning, allocation, and disaster prevention, therefore, become increasingly important. One of the most important hydrological data in water resources planning and management is river discharge. The conventional way is to use semi-intrusive instruments to obtain the section depth and vertical flow profile to estimate the discharge. The contact method involves a great deal of manpower and can pose serious hazards by floods and extreme events. In recent years the application of non-intrusive methods to measure hydrological data has become the mainstream, such as Large-Scale Particle Image Velocimetry (LSPIV) used to measure the surface velocity of rivers and estimate the discharge. The unknown water depth, however, become obstacle for this image technique. A method combined with LSPIV to obtain the bathymetry was proposed in this study. The continuity equation of shallow water equation combined with LSPIV technique was conducted to measure the bed elevation in the 1 m wide flume. The two-dimensional surface velocity data obtained from LSPIV were used to derive the two-dimensional bathymetry data by using the Leap-frog scheme in a pre-defined grid under the constraints of Courant-Friedrichs-Lewy (CFL) and solving the continuity equation. The bed elevation data of this study were verified using the conventional point gauge measurements. The results showed that the proposed method was effective in estimating the variation of the bed elevation of the flume, especially in the shallow water level, with an average accuracy of 90.8%. The experimental results also showed that the non-intrusive imaging technique combined with the numerical calculation to solve the water depth and bed elevation is a feasible method.