Hydrological models are being increasingly considered as reliable tools in providing insights to decision makers on potential scenarios of catchment management when climatic and anthropogenic factors are changing. In this context, an appropriate identification of the physical processes involved in rainfall-runoff transformation, starting from the soil moisture conditions of the basin, is required. This paper, addressing the soil moisture issue, investigates, for a pluriannual period, the scenarios for part of a natural channel network which is fundamental for water resources management in the upper Tiber River basin, Central Italy. The analysis is based on the extended formulation of the Tiber River basin semi-distributed hydrological model, including a new component for the soil water balance, which represents a useful tool for runoff prediction in a climatic and land use changing scenario. In particular, the model permits, for each single uniform unit (sub-basin), to assess both the average soil moisture condition and the different runoff components at the basin outlet. The model requires an estimate of a few physically based parameters and hydrological quantities routinely measured, as input data. The model performance is found quite accurate in terms of runoff prediction at gauged sections, belonging to the investigated channel network. The daily discharge assessment during the pluriannual period has allowed for evaluating the contribution of each river branch and hence the suffering temporal ranges of the channel system for low flows.