This paper explores the use of the rain-on-grid (or direct rainfall) method for flood risk assessment at a basin scale. The method is particularly useful for rural catchments with small vertical variations and complex interactions with man-made obstacles and structures, which may be oversimplified by traditional hydrologically based estimations. The use of a hydrodynamic model solving mass and momentum conservation equations allows the simulation of runoff over the watershed at a basin scale. As a drawback, more detailed and spatially distributed data are needed, and the computational time is extended. On the other hand, a smaller number of parameters is needed compared to a hydrological model. Roughness and rainfall loss coefficients need to be calibrated only. The direct rainfall methodology was here implemented within the two-dimensional HEC-RAS model for the low-land rural, and ungauged, watershed of the Terdoppio River, Northern Italy. The resulting hydrographs at the closing section of the watershed were compared to synthetic design hydrographs evaluated through pure hydrological modelling, showing agreement on the peak discharge values for the low-probability scenarios, but not on the total volumes. The results in terms of water depth and flow velocity maps were used to create flood hazard maps using the Australian Institute for Disaster Resilience methodology. The Index of Proportional Risk model was then adopted to generate a basin-scale flood risk map, by combining flood hazard maps, damage functions for different building-use classes, and the value of reconstruction and content per unit area.