Korean water quality managers are required to promptly develop national assessment standards for freshwater sediment quality due to the Four Major River Restoration Project in Korea in 2009. We conducted this study to develop sediment management standards (SMSs), determining obviously and severely polluted sediment, which could have adverse impacts on water quality and aquatic ecosystem. The SMSs values were derived from the 95th percentile of concentration distribution for organic matter and nutrients in sediment quality database. For the SMSs of metals, foreign sediment quality guidelines (SQGs) were adopted. As a result, 13% for loss on ignition (LOI), 1,600 mg/kg for total phosphorus (TP), and 5,600 mg/kg for total nitrogen (TN) were set as the SMSs for freshwater sediment in Korea. These values were higher than the range of heavily polluted sediment from USEPA Region 5 guideline derived by the similar approaches for the Great Lakes harbor sediments, and similar or lower than the severe effect level (SEL) from provincial sediment quality guideline (PSQG) of Ontario, Canada by screening level concentration (SLC) approach. However, SMSs in the present study are appropriate considering the concentration ranges and the Korean SMSs’ definition for freshwater sediments in Korea. The Puget Sound marine sediment cleanup screening level (CSL) in Washington State, USA were adopted as the Korean SMSs for As (93 mg/kg), Cd (6.7 mg/kg), Cr (270 mg/kg), Cu (390 mg/kg), Pb (530 mg/kg), and Zn (960 mg/kg) in freshwater sediments. Hg concentration (0.59 mg/kg) of CSL was too low to determine the polluted freshwater sediments in Korea, and the SEL of Ontario, Canada for mercury concentration (2 mg/kg) was selected as the SMS for Hg. These values were found reasonable through the assessment of applicability with the datasets from locations directly affected by obvious point sources. These results indicate that SMSs for organic matter, nutrient, and metals derived within the present study can successfully determine obviously and severely polluted sediment in Korea. However, the SMSs have limits to specifically determine the effects of polluted sediment on water quality and aquatic ecosystem in Korea. Thus, we will revise and specify SMSs considering those effects and further sediment quality assessment framework in the near future.