River water quality and organisms have a very close relationship with the human living environment and health, so it is very important to ensure and maintain the ecological integrity of the aquatic ecosystem. In that sense, benthic diatoms have relatively little mobility, can explain the effects of long-term exposed pollution sources, and are very suitable indicator organisms for river ecosystem evaluation. Diatom ecologists have been developed various diatom indices to assess water quality and stream ecosystem over the world. However, they so far have insufficient identification of taxa, are strongly regional, and are difficult to apply as they are domestically. Unfortunately, there has not been developed an independent diatom index suitable for the Korean stream. Therefore, management of water quality and aquatic ecosystem suitable for domestic rivers can be made, and development or improvement of comprehensive multivariate diatom index for the integrated assessment of water quality and aquatic ecosystem is urgently needed.