The skin effect is an important issue associated with a loss of hydraulic efficiency in pumping systems. In this paper, a comprehensive study is conducted to determine how the evolution of the skin effect over time affects the productivity and functionality of brine exploitation systems in a crystalline halite aquifer. Several double-packer system tests have been interpreted via groundwater modeling to hydrogeologically characterize the investigated aquifer. A numerical groundwater flow model that accounts for the heterogeneity of the multilayer halite aquifer and the transient well skin effect on the brine exploitation system is presented to explain the continuous drawdown during three months of constant-rate brine extractions. Numerical results obtained suggested that an exponential decay function of permeability over time was required in a wellbore skin zone to reproduce numerically experimental observations during brine exploitation. The empirical exponential function obtained specifically for this case study was generalized, and coefficients considered were discussed to infer their physical and geochemical dimensions related to the mixing process triggering heterogenous reactions responsible for the hydraulic loses. Our results will be useful for predicting the spatial and temporal losses of hydraulic efficiency and for evaluating the lifetimes of brine exploitation infrastructure.