Pronounced spatio-temporal variability of rainfall in semi-arid basins remains a central challenge for rainfall–infiltration–runoff modeling, particularly in ungauged or newly instrumented catchments where continuous soil-moisture data are unavailable. This study evaluates the comparative predictive performance of the SCS-CN and Green-Ampt (GA) infiltration methods, implemented within HEC-HMS at the sub-basin scale, using eight rainfall–runoff analysis time windows recorded during the 2020–2025 rainy seasons within a monitoring network operational since October 2019 in an instrumented semi-arid basin in Mexico. A blind-validation framework was adopted: parameters for both methods were derived a priori from tabulated sources indexed by land use, hydrologic soil group, soil textural class, and locally supported by textural analysis at three depths per sub-basin, in situ testing of saturated hydraulic conductivity, and gravimetric determination of field capacity; the initial moisture content required by GA was set equal to the measured field capacity (θ_i = θ_fc) to equate initial conditions between the two methods. Spatially distributed rainfall was captured by four monitoring stations under a one-to-one gauge–sub-basin assignment scheme, with monthly rainfall depth varying from 22.8 to 204.9 mm across the four sub-basins. Both methods reproduced observed discharge with varying levels of agreement: SCS-CN yielded very good performance (Pearson R = 0.95; Nash–Sutcliffe efficiency NSE = 0.76), whereas Green-Ampt yielded moderate correlation but unsatisfactory NSE (R = 0.70; NSE = 0.45) against the Levelogger records. Contrary to the initial expectation that the physically based GA would outperform SCS-CN, SCS-CN yielded substantially higher performance across windows, with the two simulated discharge series differing by a mean absolute deviation of 36.9 m³/s. A systematic sensitivity analysis (±6%, ±10%, ±20% perturbations) revealed an asymmetric response: SCS-CN was highly sensitive to Curve Number perturbations (mean-deviation amplitude 65.9 m³/s), whereas Green-Ampt was nearly insensitive to its compound soil-hydraulic parameterization (amplitude 3.2 m³/s), indicating a structural limitation of the physically based method under blind validation.