The allocation of margin of safety (MOS) at a uniform rate to all areas of the unit watershed makes it very difficult to keep the load allotment stable in the area for lack of reduction measures like forest land. This study developed an equation to calculate margin of safety differentially according to the regional characteristics. The equation was formulated on the basis of the regional characteristic factors such as a load contribution factor for land use type and a site conversion factor for the unit watershed. The load contribution factor represents a contribution of loads from a particular land use. The site conversion factor was derived from the site conversion ratio of a unit watershed. Margin of safety for the non-point pollution load in the land use sector decreased by 20~25% in three river basins. The margin of safety in the unit watersheds with low site occupation ratios decreased in high rate, while in the unit watersheds with large urban area decreased in low rate. With the application of the differential margin of safety considering regional characteristics, not only the reduction of pollution loads can become lighter but also it can be easier to develop plans for Total Maximum Daily Loads (TMDLs) even where the reduction measures are not available.