This paper presents advancements to the approach for Total Maximum Daily Load (TMDL) development in Korea. The current Korean TMDL process does not directly consider uncertainty and it does not include an objective approach to allocate pollutant load reductions. This paper develops a methodology to address uncertainty by incorporating a margin of safety (MOS) based on three approaches: judgment, standard error of loading characteristics, and uncertainty and variability of loading characteristics. In addition, three pollutant load reduction allocation approaches are compared to assess their impact: equal load, equal percent, and equity standard reductions. These two proposed additions to the TMDL process in Korea are demonstrated for a BOD TMDL development in the Anyangcheon Watershed. The results confirm the importance of incorporating uncertainty into the TMDL process and clearly illustrate the significant differences in TMDL and load allocation produced when using different approaches to estimate the MOS. Further, the comparison of the three load allocation strategies highlights the potential limitations of equal load and equal percent reduction approaches. The use of technical expert and decision maker ranking of factors create an equitable and sustainable load allocation among the sub-watersheds. It can be concluded that incorporating uncertainty and providing an objective load allocation strategy are essential elements needed for future TMDL development in Korea.