Abstract: Diatom, as a kind of autotrophic photosynthetic eukaryotic algae, is an important primary producer in aquatic ecosystem, and can reflect the average status of water environment. As the bio-indicators of the environment, Nitzschia communis, Navicula minuscula, and Gomphonema parvulum can indicate the eutrophication of waters, whereas Gomphonema angustum, Epithemia adnata, and Diatoma moniliformis can indicate the oligotrophication of waters. Cyclotella bodanica, Neidium affine, and Eunotia exigua are all the eosinophilic species that can indicate waters acidity, Aminutissimum nodusa can indicate water’s Cu concentration, and Synedra ulna can indicate the Zn concentration in waters. Some other diatoms can also indicate water’s contamination. This paper reviewed the research progress on the applications of diatom and diatom indices in river health assessment, pointed out the related existing problems, and put forward some future research directions, e.g., further perfect the classification and identification of diatoms, broadly carry out the researches of diatom indices upon different areas and conditions, pay more attention to the screening of diatom biointegrality indices, and establish a benchmark which suits for the assessment of water quality.