Runoff plays an important role in the agricultural and urbanized environments. Surface runoff is determined primarily by the amount of precipitation and by infiltration characteristics related to soil type, soil moisture, antecedent rainfall, land cover type, impervious surfaces, and surface retention. In this study, CCHE2D, a numerical model for free surface flow hydrodynamics, is applied to study the rain induced runoff and channel flow mixed problems. The main goal of this study is to incorporate rainfall as an input into the existing free surface flow model, CCHE2D; to verify and validate the CCHE2D model’s runoff simulation capability using analytical solutions and experimental data so that the model is proven to be accurate and capable of simulating rainfall induced flow and runoff; and to simulate runoff process in complex watershed using high resolution data such as LiDAR topography to validate that the model can be applicable to problems with a variety of spatial scales and complexity. Infiltration and subsurface flow is not considered throughout the study. The model’s capability of simulating the rainfall generated runoff processes is tested using analytical solutions, experimental data and field data. Comparison of numerical solutions with both analytic solutions and observed overland flows resulting from unsteady rainfalls is satisfactory. To validate the applicability of the shallow water model CCHE2D, research has been conducted using very high resolution LiDAR data in a small real world agricultural watershed in northwestern Mississippi, USA, in the Mississippi River Alluvial Plain known as the Mississippi Delta. The fine resolution of the numerical simulations resolved detailed runoff patterns in watersheds. This capability can be used for soil erosion and agro-pollutant transport and flood impact studies