Warm-season rainfall associated with mesoscale convective systems (MCSs) in the central United States is characterized by higher intensity and nocturnal timing compared to rainfall from non-MCS systems, suggesting their potentially different footprints on the land surface. To differentiate the impacts of MCS and non-MCS rainfall on the surface water balance, a water tracer tool embedded in the Noah land surface model with multiparameterization options (WT-Noah-MP) is used to numerically “tag” water from MCS and non-MCS rainfall separately during April–August (1997–2018) and track their transit in the terrestrial system. From the water-tagging results, over 50% of warm-season rainfall leaves the surface–subsurface system through evapotranspiration by the end of August, but non-MCS rainfall contributes a larger fraction. However, MCS rainfall plays a more important role in generating surface runoff. These differences are mostly attributed to the rainfall intensity differences. The higher-intensity MCS rainfall tends to produce more surface runoff through infiltration excess flow and drives a deeper penetration of the rainwater into the soil. Over 70% of the top 10th percentile runoff is contributed by MCS rainfall, demonstrating its important contribution to local flooding. In contrast, lower-intensity non-MCS rainfall resides mostly in the top layer and contributes more to evapotranspiration through soil evaporation. Diurnal timing of rainfall has negligible effects on the flux partitioning for both MCS and non-MCS rainfall. Differences in soil moisture profiles for MCS and non-MCS rainfall and the resultant evapotranspiration suggest differences in their roles in soil moisture–precipitation feedbacks and ecohydrology.