Abstract: Diatoms are one of the most important primary producers in aquatic ecosystems. Diatoms can provide carbon source for consumers in ecosystems. They are regarded as good indicators of environmental changes, due to their wide distribution, species abundance and short generation time. In this paper, we reviewed the vital role and characteristics of diatoms in aquatic ecosystems, especially in river ecosystems. We also described the responses of diatoms to environmental variables at individual, population, and community levels. The current status and prospects of diatoms (and the diatom index) in the monitoring and assessment of river ecosystem health were also discussed. We introduced the theory and history of the development of diatom indices in general, indices which are now used widely throughout the world, and particularly we discussed the diatom based index of biotic integrity (IBI) in terms of methods, principal and application. The problems associated with the application of diatom based IBI were pointed out.