Six rivers were selected as preliminary screening sites to determine the test conditions of Microtox in assessing the toxicity of the sediment. In addition, a pH range of 6.0∼6.5 was established in testing pore water, aqueous extracts and organic extracts. Each extractable fraction of sediment showed different toxicities. Therefore, in order to properly examine the toxicity in the sediment, all extractable fractions of sediment samples needed to be tested with Microtox. Thus, sediment samples were additionally collected from at least 4 secondary sites within 50∼100ｍ area of the primary sampling site to reduce any variation or deviation in toxicity assessment. From all sediment toxicity data that was collected from this study, it was concluded that the Keumho river was the most polluted with the highest sediment toxicity of all the rivers analyzed and needed further detailed research on its pollution problem.