The opening of a deep artificial and second entrance channel into the large Peel-Harvey Estuary in south-western Australia in 1994 provided a unique opportunity to determine the characteristics of the ichthyofauna of a microtidal estuary, in which tidal water movement and the rate of recovery of salinities in spring have both increased markedly. Fishes in the original entrance channel and both halves of the two large basins (Peel Inlet and Harvey Estuary), which constitute most of the total area of the estuary, were sampled using a 21·5 m long seine with a fine (3 mm) mesh bunt. The 72 337 fishes that were caught throughout the estuary and represented 43 species, comprised mainly marine species, both in terms of number of species (65·1%) and number of individuals (70·6%). The number of species and density of fishes in each region, and particularly in the basins, showed a pronounced tendency to decline from a maxima in summer to a minima in winter and then to rise in spring. Although the species composition of the fish fauna in the natural entrance channel differed significantly from that in each of the four basin regions, those within the basins were significantly different only in the cases of the southern Harvey Estuary versus both regions of the Peel Inlet. Species composition in the natural entrance channel and four basin regions each underwent conspicuous cyclical changes during the year, which reflected out-of-phase changes in the densities of certain species. Although this cyclical pattern was due mainly to changes in the densities of marine species, it was augmented by those of estuarine residents. The cyclicity, which was not evident prior to the opening of the artificial Dawesville Channel, and thus when tidal water movement within the estuary was far less pronounced, parallels the situation recorded for macrotidal northern hemisphere estuaries.