Hydraulic conductivity generally decreases with depth in the Earth’s crust. The hydraulic conductivity–depth relationship has been assessed through mathematical models, enabling predictions of hydraulic conductivity in depths beyond the reach of direct measurements. However, it is observed that beyond a certain depth, hydraulic conductivity tends to stabilize; this phenomenon cannot be effectively characterized by the previous models. Thus, these models may make inaccurate predictions at deeper depths. In this work, we introduce an innovative exponential model to effectively assess the conductivity–depth relationship, particularly addressing the stabilization at greater depths. This model, in comparison with an earlier power-like model, has been applied to a globally sourced dataset encompassing a range of lithologies and geological structures. Results reveal that the proposed exponential model outperforms the power-like model in correctly representing the stabilized conductivity, and it well captures the fast stabilization effect of multiple datasets. Further, the proposed model has been utilized to analyze three distinct groups of datasets, revealing how lithology, geological stabilization, and faults impact the conductivity–depth relationship. The hydraulic conductivity decays to the residual hydraulic conductivity in the order (fast to slow): metamorphic rocks, sandstones, igneous rock, mudstones. The mean hydraulic conductivity in stable regions is roughly an order of magnitude lower than unstable regions. The faults showcase a dual role in both promoting and inhibiting hydraulic conductivity. The new exponential model has been successfully applied to a dataset from a specific engineering site to make predictions, demonstrating its practical usage. In the future, this model may serve as a potential tool for groundwater management, geothermal energy collection, pollutant transport, and other engineering projects.