Regional groundwater flow in high mountainous terrain is governed by a multitude of factors such as geology, topography, recharge conditions, structural elements such as fracturation and regional fault zones as well as man-made underground structures. By means of a numerical groundwater flow model, we consider the impact of deep underground tunnels and of an idealized major fault zone on the groundwater flow systems within the fractured Rotondo granite. The position of the free groundwater table as response to the above subsurface structures and, in particular, with regard to the influence of spatial distributed groundwater recharge rates is addressed. The model results show significant unsaturated zones below the mountain ridges in the study area with a thickness of up to several hundred metres. The subsurface galleries are shown to have a strong effect on the head distribution in the model domain, causing locally a reversal of natural head gradients. With respect to the position of the catchment areas to the tunnel and the corresponding type of recharge source for the tunnel inflows (i.e. glaciers or recent precipitation), as well as water table elevation, the influence of spatial distributed recharge rates is compared to uniform recharge rates. Water table elevations below the well exposed high-relief mountain ridges are observed to be more sensitive to changes in groundwater recharge rates and permeability than below ridges with less topographic relief. In the conceptual framework of the numerical simulations, the model fault zone has less influence on the groundwater table position, but more importantly acts as fast flow path for recharge from glaciated areas towards the subsurface galleries. This is in agreement with a previous study, where the imprint of glacial recharge was observed in the environmental isotope composition of groundwater sampled in the subsurface galleries. Copyright © 2012 John Wiley & Sons, Ltd.