This paper presents results of a database compilation for indicator species from fresh and brackish aquatic habitats. Information about aquatic species ecology was collected from international guides, our own research during the last 40 years, as well as from monographs and electronic resources describing the ecology of diverse taxonomic groups of organisms. Most of the species represented in the database belong to algae and cyanobacteria taxa, but the ecology of some other aquatic organisms, such as higher plants, moss, and bacteria is also documented. Altogether, 8475 algal, cyanobacteria, plants, and other aquatic inhabitants from 36 taxonomical divisions are represented in the database. Ecological information is given according to 12 indication methods for the following parameters: confinement to the substrate, temperature, oxygen, and the mobility of the water mass, preferences to water pH, water salinity, saprobity according to Watanabe, saprobity according to Sládeček, saprobity index (SI) according to Sládeček, trophic states, nutrition types and several others. This comprehensive database is scheduled for publication in a book and can be used by a wide spectrum of ecologists for the purpose of aquatic ecosystem assessment and monitoring of water quality based on bioindication methods.