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Lake Gregory is a large semi-permanent lake system in arid north-western Australia. Its catchment extends into humid areas and as a result the lake has dried only twice in the last 25 years. Although the system is mostly fresh, parts of it become saline as they dry. We identified aquatic invertebrates and undertook chemical analysis of water samples from several sites at Lake Gregory in 1989, when the main water-body was saline, and in 1991 and 1993, after the system had flooded and was fresh. During the period 1989-1993, salinities varied from 0.1% to 82%, and ionic composition ranged from strong sodium chloride dominance, in saline water and fresh water of the eastern part of the system, to bicarbonate dominance in fresh water of the western area. At least 174 invertebrate species were recorded, including two mollusc species that were never collected live. This species richness is much higher than that recorded from other Australian arid zone lakes, probably owing to long periods of inundation with fresh water. The fauna was dominated by insects (42 per cent of total species richness), crustaceans (27 per cent) and rotifers (22 per cent). Most species (160) were restricted to fresh water; only 12 species were found in saline water. Only one ostracod occurred in saline conditions, although ostracods are a dominant group in Australian saline lakes. Among species restricted to fresh water, the proportion of rotifer and protozoan fauna that occurred in bicarbonate-dominated water was greater than the proportion of insect, crustacean and hydracarine fauna that did so.