This article provides an overview of the species composition, habitats, and diversity of phytoplankton in Estonian streams during 1991-2001. A checklist is presented containing 443 taxa with their occurrence and habitats. Diatoms were the most numerous group, followed by green algae and cyanobacteria, and nanoplanktonic flagellates were ubiquitous. The phytoplankton of Estonian streams was frequently supplemented with suspended epiphytic and epilithic diatoms. The number of taxa per litre varied in the range from 7 to 56 (median 19) and showed a weak upward trend with increasing trophic degree of stream water.The phytoplankton compound quotient (PCQ) ranged from 0.7 to 22.5 and correlated weakly with trophic degree, BOD5 concentration and stream order.