An intermediate regulator regulates the water demand flow to meet the maximum water requirements. The shortage in water demands fulfills the needs of agricultural drains after required water treatment. The upstream water levels at the two sides in the longitudinal direction of the regulator determine the flow direction through this structure. Since the movement of water is in two directions, the stilling basin must be symmetrical. The effect of double square baffles with different heights and widths located at the mid-distance of the stilling basin on the submerged hydraulic jump characteristics downstream gates are investigated. Various components, such as relative baffle heights and widths, were studied experimentally under different flow conditions. The experiments were conducted on a 16 m long, 66 cm wide, and 64 cm deep flume. One-dimensional momentum and continuity equations are applied to the control volume to deduce the theoretical equation of the relative depth and energy loss of the submerged jump. The dimensional analysis was used to define the affecting dimensionless variables under the studied phenomenon. The square baffle shape model with a relative width equal to unity is the optimal width from the jump characteristics point of view. In addition, as the relative height of the baffle increases, the performance of the hydraulic jump characteristics enhances within the experimental limits of this study (the relative baffle height ≤ 3.01). The average decrease of the jump’s relative depth and length is (22%–25.8%), respectively, and the average increase of the relative energy loss is 20.8% at the inlet Froude number equals 4. The average percentage error between theoretical and experimental data was ±10% and ±8% for the relative depth and energy loss of the submerged hydraulic jump, respectively.