Natural hydrological disturbances in streams may reduce biomass and species richness and change community composition within streams. Disturbances can also affect beta diversity among streams if their effects are species specific or vary across sites. We investigated the effect of a natural flood on species richness, community composition and among-streams beta diversity of benthic diatoms (total community and three functional groups: low profile, high profile and motile) of seven streams in New Zealand. Sampling occurred shortly before, 10 days after and 40 days after the flood. Species richness of the total diatom community did not change after the flood. The high-profile group was the only one whose species richness declined after the flood, whereas species richness of the low-profile group increased. Community composition changed after the flood, mostly as a result of species replacement rather than richness differences over time. Finally, among streams beta diversity did not change after the flood, suggesting that variation in species composition of benthic diatoms among streams may be maintained in the face of flood disturbances.