In 2012, the regional hydrogeological model (HM) of Latvia has been completed by Riga Technical University. HM covers 475km300km area. It includes the territory of Latvia, the Gulf of Riga (active zone) and border areas of neighbouring countries (passive zone). The both zones are separated by the 4km vide border. Steady state HM simulates the active groundwater zone that contains drinking groundwater resources for Latvia. HM includes 25 geological layers. The plane approximation step of HM is 500 metres . The HM body is enveloped by its top and bottom surfaces, but HM outer vertical sides are constituted by the shell. On all HM outer surfaces, piezometric boundary conditions are fixed. On the HM top and bottom surfaces, accordingly, the relief (ground surface elevations) and the Pernava aquifer D2pr head distribution maps are used, as boundary conditions. The relief map also represents the geometrical top surface of HM. Initially, the HM shell surface acts as an impermeable barrier for a groundwater trans-boundary flow, because, outside the HM body, the area of HM inactive zone is located. To overcome this drawback, the distribution of boundary conditions for the HM shell must be found. The distribution are set on the middle line of the HM border-zone where the real values of trans-boundary flows for aquifers must be recovered.