This study describes the ecology of mesozooplankton in the shallows of the large central basin area of the Swan-Canning Estuary on the microtidal lower west coast of Australia during the mid-1980s when, as in most other south-western Australian estuaries, it was mesotrophic. As the vast majority of species reproduce within the estuary and there is a lack of a net upstream flow of bottom water during each tidal cycle to facilitate selective tidal transport, the populations of those species are considered autochthonous. Species restricted to the estuary accounted for 63% of the total number of species and 83% of abundance. Contributions by tychoplankton to total number of species (68%) and individuals (59%) exceeded the corresponding values of 18 and 39% for holoplankton and 14 and 2% for meroplankton. Low meroplankton values result from a paucity of benthic macroinvertebrate species with planktotrophic development. Comparisons with data for the shallow basin areas of the nearby highly eutrophic Peel-Harvey Estuary were used to indicate how mesozooplankton in the microtidal estuaries respond to excessive nutrient enrichment. The mean number of species in the Swan-Canning was essentially the same as in the Peel-Harvey, whereas concentrations were only half, reflecting the lower productivity of the former estuary. However, concentrations of the four most abundant species in the Swan-Canning, the amphipod Grandidierella propendatata, the calanoids Gladioferens imparipes and Acartia cf. clausi and a harpacticoid species, exceeded those of these species in the Peel-Harvey by between 1.6 and 11.7 times. Greater concentrations in the Swan-Canning were attributable to this mesotrophic system not undergoing the reduction in oxygen concentrations and/or environmental degradation, to which these species are susceptible. In contrast, concentrations of the amphipods Corophium minor and Tethygenia elanora and large nematodes, which are tolerant of degraded environmental conditions, were greater in the Peel-Harvey. Holoplankton made a far greater contribution in the Swan-Canning than Peel-Harvey, due to substantial numbers of copepods that benefit from good environmental conditions. Mesozooplankton composition in both estuaries underwent cyclical changes during the year due to time-staggered differences in seasonal concentrations of various species. Cyclical changes and variations in composition were more closely related to measured environmental variables in the Swan-Canning than Peel-Harvey estuaries. The concentrations of many species were greater at night than during the day presumably reflecting a nycthemeral response and/or low nocturnal oxygen concentrations at the bottom of the water column.