Surface runoff and infiltration partition is a primary process of hydrologic cycle. Here, we compare four different surface runoff and infiltration partition methods within a Richards-equation-based SWAT model (RSWAT) to understand their effects on watershed modeling. Four surface runoff and infiltration partition methods include a Daily Curve Number method (DCN-RSWAT), a Hourly Curve Number method (HCN-RSWAT), a Green-Ampt method (GA-RSWAT), and an Effective Infiltration Capacity method (EIC-RSWAT). These four versions of RSWAT and a Daily Curve Number based original SWAT (DCN-SWAT) were applied to simulate daily stream flow and baseflow (from 2001 to 2015) at the Tuckahoe Creek Watershed (TCW) and Greensboro Watershed (GW) in Maryland, US. The global sensitivity analysis algorithms within SWAT-CUP was used to identify sensitive parameters, and the Sequential Uncertainty Fitting algorithm version 2 (SUFI-2) was used to analyze uncertainty for different models in both calibration and validation periods. Comparison of the results from different models highlight the sensitivity of watershed modeling to the differences between surface runoff and infiltration partition methods. In general, DCN-RSWAT outperformed other versions of RSWAT and the standard SWAT model with reduced daily flow rate perdition uncertainty and improved simulation of daily baseflow in both test watersheds. We anticipate the numerical experiments examined here will provide new insights into better practices in choosing surface runoff and infiltration partition methods for SWAT and other watershed models, thereby supporting sustainable water resources assessment and management.