<p>Groundwater inflow constitutes a critical challenge in rock tunnel engineering. This study systematically investigates the coupled effects of fracture spatial distribution and rock matrix permeability on tunnel water inflow using a novel embedded discrete fracture model based method. A set of quadratic regression models is established to delineate the relationship between inflow rate and fracture distribution parameters over a wide range of fracture-to-matrix permeability ratios (<i>k</i>_f/<i>k</i>_m). Results demonstrate that fracture aperture, spacing, and their interaction dominate the inflow across all permeability ratios. Analysis of variance further reveals a threshold-dependent behavior: coupled effects are significant below a critical <i>k</i>_f/<i>k</i>_m value but decay markedly above it. This threshold decreases with larger aperture and increases with wider spacing, yet remains nearly independent of fracture dip angle. Moreover, when <i>k</i>_f/<i>k</i>_m is below the threshold, aperture and spacing exert greater influence on tunnel inflow at lower permeability ratios, while <i>k</i>_f/<i>k</i>_m gains influence under larger apertures and smaller spacings. Finally, a case study of Nanwan Tunnel shows that matrix permeability plays a dual role—increasing the mean inflow rate while reducing uncertainty from stochastic fracture distribution.</p>