A new monitoring system using horizontal acoustic Doppler current profiler (H-ADCP) measurements and river flow simulation was developed to attain accurate and continuous monitoring for river discharge at a low cost. The H-ADCP can measure the velocity profile along a horizontal line. In the numerical simulation the measured velocities were interpolated and extrapolated for a river cross section. As part of the simulation, we developed a river flow model with a new approach for data assimilation to reflect rationally measured velocities in numerical simulations. The new computational method is referred to as the dynamic interpolation and extrapolation (DIEX) method. To confirm the fundamental performance of the present system, H-ADCP measurements were performed in the middle reach of the Edo River in Japan, and the river discharge was then evaluated using the DIEX method. The calculated velocity and discharge were compared with the results measured using an ADCP and a Price current meter. The vertical and lateral distributions of the calculated velocities are in good agreement with the measured results. The discharge calculated by the DIEX method is in good agreement with the observed data. The root mean squares of the relative error for the calculated discharge is 4.9%, showing that the accuracy of the DIEX method is the same as the conventional method using point sensors such as a Price current meter. The present monitoring system achieves accurate, automatic, and continuous monitoring of river discharge at a lower cost than direct measurement methods for discharge.