<p>The fractured mountain aquifers provide drinking water to millions of the world population but the instruments in preventive vulnerability examination of low-background systems are not well advanced. The paper formulates and field tests a framework of vulnerability screening which combines regular hydrochemical monitoring with modelling of groundwater flow and solute transport to assist in adaptive groundwater management. The structural form is shown in a representative fractured Himalayan aquifer in which natural uranium is a process-sensitive geochemical tracer of groundwater transport behaviour, and is not a contaminant of concern. On-site sampling shows that the background system is persistently low and the uranium concentrations are often below the analytical detection limit (0.2&#xa0;µg L^− 1). Springs and handpumps showed 8.8 and 13.3% detection, respectively with the highest values of 0.95 and 1.40&#xa0;µg L^− 1, respectively. In order to elucidate these observations in more than a descriptive monitoring process, a steady-state groundwater flow and solute transport model was constructed based on representative hydrogeological parameters of fractured crystalline aquifers. Model analysis indicates that under baseline conditions, the uranium accumulation is restricted by advective-dominated transport and short residence times (mean linear velocity = 0.312&#xa0;m/day). The sensitivity analysis shows that change in recharge strength or groundwater abstraction could alter flow paths and residence times and may alter system vulnerability even at low background concentrations. The combination of the field and modelling output justifies the transition of the conventional concentration-threshold measurement to the transport-dynamics-based vulnerability measurement of preventive groundwater management in fractured mountain aquifer systems.</p> Graphical Abstract <p></p>