Fracture zones, which are commonly saturated with water, pose significant risks during underground construction and the ongoing maintenance of infrastructure projects. Detecting such objects and monitoring their stability usually require surface geophysical methods over rough terrains that are slow and expensive, sometimes even impractical if the fracture zone is underwater. In this work, we propose using the semi-airborne magnetometric resistivity (SA-MMR) method to monitor the water content in the fracture zone rapidly. SA-MMR combines the advantages of efficiency from drone-borne geophysics and high data quality because of the measurements of a steady-state magnetic field by high-precision total-field magnetometers. We design our model based on an actual water gushing accident during the tunnel construction. The accident happened when the water from a reservoir above the route gushed into the tunnel through a weathered fault zone. In our synthetic survey, we utilize a set of electrodes that act as current sources, strategically placed along the strike of the fault; the total-field magnetometer, which is suspended 5 meters above the terrain using a drone that covers the entire survey area; two identical surveys are carried out before and after the fault’s water content increases. Our 3D forward modeling indicates that despite the low-resistivity water layer above the fracture zone, the SA-MMR data anomaly can be as large as 16 nT for a 10 A source current. The magnitude of the detected anomaly in question surpasses the noise level of contemporary airborne total-field magnetometers by multiple orders of magnitude, and our study has shown that SA-MMR has great potentials in quickly and economically mapping the variation of water content in water-rich fracture zones.