The new proposed railway network in the city of Bratislava, which is supposed to be connected to the airport, is an integral part of Trans-European Network for Transport .Certain section of the planned railway should be constructed along Carpathian Mountains through underground tunnels. However, the construction of this underground tunnel will adversely affect the groundwater flow regime. Therefore, it was necessary to establish a 2D finite element numerical model to evaluate the implementation of this railway tunnel on the groundwater regime as well as means of technical measures to reduce the impacts. The paper presents the model result, analyses, prognosis as well as possible methods to control the groundwater level regime in the aquifer that could be affected by the railway tunnel construction.