One of the goal for the preparation of Nemunas RBD management plan is to provide a description of the current state of RBD, including the assess of groundwater discharge into surface water bodies. Groundwater discharge into surface water bodies in Nemunas RBD was carried out in four independent mathematical models for individual groundwater bodies (GWB). Models included shallow groundwater, surface water and deeper laying confined aquifers. The obtained results later were combined. Transmissivity values and recharge rates of shallow groundwater aquifer have been revised by mathematical modelling. Sources of groundwater runoff formation, i. e. an input of groundwater flow from the unconfined aquifer and deeper confined aquifers into surface water bodies, were evaluated. In addition groundwater discharge variation throughout the river length was itemized.