Seepage is the primary cause of dam failures. Conducting regular seepage analysis for dams can effectively prevent accidents from occurring. Accurate and rapid determination of seepage parameters is a prerequisite for seepage calculation in hydraulic engineering. The Whale Optimization Algorithm (WOA) was combined with Support Vector Regression (SVR) to invert the hydraulic conductivity. The good point set initialization method, a cosine-based nonlinear convergence factor, the Levy flight strategy, and the Quasi-oppositional learning strategy were employed to improve WOA. The effectiveness and practicality of Improved Whale Optimization Algorithm (IWOA) were evaluated via numerical experiments. As a case study, the seepage parameters of the Dono Dam located on the Baishui River in China were inversed, adopting the proposed inversion model. The calculated seepage field was reasonable, and the relative error between the simulated head and the measured value at each monitoring point was within 2%. This new inversion method is more feasible and accurate than the existing hydraulic conductivity estimation methods.