River discharge is traditionally required with a lot of measurements and data. However there are areas where discharge data is not available. In this research a tool is developed based on hydraulic geometry relations to estimate the discharge of a river in bank full state near Narok, Kenya. With the help of the Global Navigation Satellite System (GNSS) coordinates are converted in to cross-sections of the river in a bank full state. Discharges are assumed and verified through the hydraulic geometry relations of the cross-sections. These discharges are simulated in Super-Fast INundation of CoastS (SFINCS) to simulate the flash floods of Narok and an accurate estimate of the river discharge in a bank full state was obtained.