Presented paper deals with the hydraulic assessment of groundwater flow in the area affected by the realization of the hydraulic gate on the Klátov branch and in the adjacent territory of a dike, which is located on the right-side of Little Danube. This hydraulic assessment is part of the project of the Slovak Water Management Enterprise, which also aims to increase the height and seal the dike on the right-side of the Little Danube. Generally, the project is divided into three phases (Phase I, II and III) to implement different technical measures to protect the area from flooding. The assumption for the execution of the technical measures of the mentioned three project phases is a continuous flood protection of part of the Žitný ostrov area around the Little Danube and the Klátov River branch in the reach from Kolárovo to Jahodná town. Therefore, a 3D mathematical model was created to simulate groundwater flow by changing boundary conditions of surface water flow during flood periods.