This paper deals with the use of diatom indices in the assessment of streams in Estonia. The problem addressed is how rational it is to determine different types of streams or stream reaches based on diatom research. At the moment, there are five different typologies of running waters in Estonia, two of which are analyzed here. Diatom indices can be employed to assess the ecological quality of water but not the status or type of stream. The most promising diatom indices for such assessment are the Trophic Diatom Index, Watanabe Index, Descy Index, and Schiefele & Schreiner Index.