The paper attempts to assess the possibility of using typical check structures equipped with sluice gates to measure the volumetric flow rate in the irrigation channels. The submerged flow through the sluice gate was considered. Experimental tests on a model of typical check structure in 1:2 scale were carried out. The conducted analyzes confirmed the possibility of using discharge equation for submerged flow through the sluice gate to estimate the water flow rate in the irrigation channels. In order to obtain accurate values of flow rate, the downstream tailwater depth should be measured at the appropriate distance from the sluice gate. For different values of gate-opening height, the downstream water depth measurement locations allowing for a correct flow estimation were indicated. This approach might be useful in calibration of other designs of sluice gates for flow measurements.