The macrobenthic invertebrates in the shallow (<0·5 m), medium-depth (0·75–1·0 m) and deep (2·0–2·5 m) waters of the lower and upper regions of the large basin of the seasonally closed Wilson Inlet were sampled, using corers, in each season between the winters of 1989 and 1990. The fauna was dominated by capitellid, spionid and nereid polychaetes and mytilid, venerid and tellinid molluscs. Almost 75% of the total numbers were contributed by the polychaetes Heteromastus filiformis (Claparède) (30·2%), Capitella capitata (Fabricius) (17·4%), Prionospio cirrifera (Wirén) (7·9%) and Boccardia chilensis (Blake & Woodwick) (5·4%), and the gastropod Hydrococcus brazieri (Tenison Woods) (12·4%). The numbers of species recorded in Wilson Inlet (41) were relatively very low for an estuary. This presumably reflects (i) the low salinities, which would restrict colonization by stenohaline marine species, (ii) the prevention of recruitment from the sea by the closure of the estuary mouth during the summer, at which time many macrobenthic species are producing pelagic larvae, (iii) the very limited tidal movements, and thus mechanisms for transporting larvae from the sea, when the estuary mouth is open, and (iv) the lack of a pronounced salinity gradient and the small variation in sediment composition along the estuary. Characteristics (ii–iv), together with the dispersal of pelagic larvae within the basin by wind mixing, would also account for the fact that faunal composition was influenced less by the region within the basin than by water depth. The densities of species, such as Ceratonereis aequisetis (Augener), Capitella capitata and H. brazieri, were greater in the shallow and medium depths than in deeper water, while the reverse pertained with P. cirrifera. Since densities of the first three species are correlated with the biomass of Ruppia megacarpa Mason, the greater amounts of this aquatic macrophyte in the shallow and medium-depth waters may thereby provide more food and/or protection from predators in those waters than would be the case in deep water. In contrast, P. cirrifera, which is a detritivore, would benefit from the greater proportion of particulate organic material in the deep waters. The greater habitat complexity in the shallow and medium-depths, that is provided by the greater amounts of R. megacarpa and shell debris in those waters, was associated with a greater species richness, diversity, density and biomass of benthic invertebrates. The composition of the fauna underwent cyclical changes, which were related, in part, to the patterns of recruitment of certain major taxa following spawning.