Accurate characterization of aquifer hydrogeological parameters is critical for sustainable groundwater resource management. Traditional methods such as pumping tests often assume aquifer homogeneity and require substantial resources, limiting their applicability for large-scale heterogeneous systems. This study proposes a novel approach to estimate the spatial distribution of hydraulic conductivity (T) and specific storage (Ss) in the Qingtongxia Irrigation Area, utilizing canal stage fluctuations as natural stimuli. By analyzing high-frequency groundwater level responses from monitoring wells during irrigation channel operations, we employed a Sequential Linear Estimator (SLE) method combined with canal stage tomography to invert aquifer parameters. The results demonstrate that the inverted hydraulic conductivity distribution aligns well with lithological variations and historical data, showing higher values in the southern alluvial fan and lower values in the northern plains. The SLE method effectively captured aquifer heterogeneity, with RMSE and correlation coefficients between pumping test and inversion results improving to 1.81 and 0.76 after excluding outliers. This work highlights the potential of natural stimuli (e.g., irrigation-induced canal fluctuations) for basin-scale hydrogeological parameter estimation, offering a cost-effective alternative to traditional methods. The findings provide valuable insights for groundwater modeling and resource management in arid regions with intensive irrigation systems.