An ArcGIS based unsaturated-saturated nitrogen transformation and transport software ArcNLET has been established. This software considered the nitrogen transformation and transport processes from point contamination sources infiltrating into soil, then arriving at the water table and continuing to transport along the groundwater flow. One-dimensional vertical water flow and nitrogen transport equations were solved to obtain the nitrogen concentrations at the water table. The groundwater flow was assumed as the two-dimensional horizontal flow. The reactive nitrogen transport equations of ammonium and nitrate were solved by the analytical solution. Then the nitrogen loads to water bodies were calculated. It was applied to estimate the nitrogen load to surface water bodies in Julington Creek watershed in Florida State U.S. The results showed the strong spatial variability of nitrogen concentration at the water table below each point source, which demonstrated the necessity of estimating the soil nitrogen transport due to the complex topography and soil characteristics. Ammonium contributed 26% of total nitrogen loads to surface water bodies. It indicated that the nitrogen contamination risk would be under-estimated if ignoring the ammonium in the aquifer. This software can provide the quantitative estimation of the nitrogen loading to surface water bodies, which is hard to be measured. The modules can be chosen independently according to the requirements of users. ArcGIS provides the pre- and post- processing results visually and easily. The model owns great potential value to be used in the regional nitrogen loading calculation with point contamination sources.