Agricultural non-point source pollution is increasingly an important issue affecting surface water quality. Currently, the majority of the studies on nitrogen loss have focused on the agricultural field scale, however, the response of surface water quality at the watershed scale into the nitrogen loss at the field scale is poorly understood. The present study systematically reviewed the critical processes and major factors that nitrogen transport from farm fields to surface water bodies. The critical processes of farmland nitrogen entering surface water bodies involve the processes of nitrogen transport from farmland to ditches and the transformation processes of nitrogen during migration in ditches/rivers. Nitrogen transport from farmland to ditches is one of the prerequisites and critical processes for farmland nitrogen transport to surface water bodies. The transformation of nitrogen forms in ditches/rivers is an intermediate process in the migration of nitrogen from farmland to surface water bodies. Nitrogen loss from farmland is related to soil storage and exogenous inputs. Therefore, nitrogen input management should not only consider the current input, but also the contribution of soil storage due to the historical surpluses. Ditches/rivers have a strong retention capacity for nitrogen, which will significantly affect the process of farmland nitrogen entering surface water bodies. The factors affecting nitrogen transformation in river/ditches can be placed in four categories: (1) factors affecting hydraulic retention time, (2) factors affecting contact area, (3) factors affecting biological activity, and (4) forms and amount of nitrogen loading to river/ditches. Ditch systems are more biologically (including plants and microbes) active than rivers with biological factors having a greater influence on nitrogen transformation. When developing pollution prevention and control strategies, ecological ditches can be constructed to increase biological activity and reduce the amount of surplus nitrogen entering the water body. The present research should be valuable for the evaluation of environment impacts of nitrogen loss and the non-point source pollution control.