Unicellular flagellate or amoeboid organisms. Most species are phagotrophic (or osmotrophic), but a part of the Euglenophyceae (e.g. Euglena) is photosynthetic using green chloroplasts via secondary symbiosis with a green plant. In some species the mitochondrion is reduced, thus they live in anaerobic emvironments such as sediments and gut of animals. Some excavates such as Trypanosoma (Euglenozoa), Giardia (Trepomonadea) and Trichomonas (Parabasalia) infect and damage humans.

Excavates basically possess two or four flagella inserted subapically and a ventral groove supported by complex microtubular roots. The ventral groove works as a cytostome. However, some excavates such as Euglenozoa, Parabasalia and oxymonads transformed from this basic form (e.g. lost of the groove). Most species of the Percolozoa possess the vegetative amoeboid cells. Mitochondrial cristae, if present, are usually discoid, but some species possess flat or tubular cristae. In the Trichozoa and Anaeromonads the mitochondria transformed to mitosomes or hydrogenosomes to lose mitochondrial genome, cristae and the ability of aerobic respiration.　Asexual reproduction by means of binary fission. Acrasis (Percolozoa) forms a fruiting body and spores (thus the organism was formerly classified in cellular slime molds). There are few reports on the sexual reproduction of excavates, but unique sexual reproductions are reported in the oxymonads.

The Excabata is proposed based on their ultrastrucural features. Although the monophylies of some clades (e.g. Trichozoa, Discicristata + Loukozoa, Anaeromonada) are supported by molecular phylogenetic studies, the monophyly of whole excavates is unsettled.