A novel type of hydraulic structure is proposed for rainwater harvesting in an arid area of Jordan. The project is to develop an irrigation scheme near the Dead Sea, where low annual precipitation and high salinity are the major concerns. The scheme consists of an irrigated farm, a reservoir, and an intake structure to divert ephemeral flood flows into the reservoir. The harvested water is expected to be fresh in comparison with the groundwater in the vulnerable freshwater lens. This research focusses on hydraulic design and actual construction processes of the structure. The structure consists of a gutter cutting across a 16 m wide valley bottom and a conveyance channel of 60 m long to guide the water into the reservoir. The conveyance channel is equipped with a spillway part. As a result of level surveys and hydrological considerations, it was revealed that the structure should have a width of 1.6 m and supercritical flows should be dominant. Details of structure dimensions were designed with numerical and model experiments. A finite volume scheme for the two-dimensional shallow water equations was used to numerically reproduce the whole flow field during a rainwater harvesting event with the maximum design discharge. The numerical scheme employs special fluxsplitting and data reconstruction techniques that realize stable computation of very shallow transcritical flows. A distorted hydraulic model with 1/8 horizontal scale and 1/1 roughness scale was constructed in an experimental station in Japan, in order to test hydraulic phenomena that the numerical method cannot represent. Then, the structure was actually constructed at the site. The channel bottoms are made of reinforced concrete, while the side walls are of concrete blocks whose sizes have been chosen according to the design. However, minor changes were made during the construction processes due to workability constraints. The numerical experiments were conducted again to confirm the actual structure showing desired performance.