Constant head injection (CHI) tests are a standard method for estimating subsurface hydraulic properties, but traditional interpretations using analytical solutions like Moye’s equation are limited by their inability to capture transient dynamics and vertical heterogeneity. This study introduces a novel transient inverse method that allows for the estimation of layer-specific hydraulic conductivities (K) in multilayered aquifers, accommodating realistic boundary conditions. Using synthetic simulations with varying specific storage coefficients (S_s) and observation times (t_rep), the method consistently produced accurate K estimates and demonstrated robustness to S_s variations. In contrast, Moye’s equation significantly underestimated K values, highlighting the limitations of steady-state approaches. The proposed method offers improved flexibility and accuracy for CHI test interpretation, making it a valuable tool for more complex, real-world aquifer systems.