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The distribution, abundance and size structure of a penaeid with tropical affinities (Metapenaeus dalli) was investigated in a temperate, microtidal estuary in southwestern Australia. Sampling was conducted every lunar month for two years at 20 sites across five regions (nine subregions) in nearshore waters by hand trawl, and at 16 sites across four regions (eight subregions) in offshore waters by otter trawl. Densities of M. dalli changed markedly seasonally, with greatest values recorded in nearshore waters from October to February, and in offshore waters from March to July. These densities also varied spatially, with the highest recorded in the Lower Canning, Middle Swan, and Upper Melville Water regions. Spearman's rank correlation showed a positive relationship between the density of M. dalli in nearshore waters and surface water temperature in all nine subregions, whilst densities of M. (lath in offshore waters were negatively correlated with bottom water temperature in most of the estuary; these correlations reflect the movement of adult prawns into shallow waters for breeding in summer, as well as the subsequent recruitment and movement back into deeper waters over the winter months. Mean carapace lengths remained relatively unchanged over the late autumn and winter months (May to August), before rapidly increasing with temperature in late spring. The spatial and temporal distribution of M. dalli differed significantly from those of other crustaceans in the estuary, particularly the penaeid Penaeus Merlicertus latisulcatus, which was concentrated mainly in the Lower and Upper Melville Water regions. The distribution of M. dalli was statistically indistinct from that of the apogonid Ostorhinchus rueppellii, which predates heavily on postlarval M. dalli, and very similar to those of two scyphozoans, Aurelia aurita and Phyllorhiza punctata, that likely predate on larval M. dalli. These findings highlight the partitioning of species within the estuary and the significance of site selection for maximising the post-release survival of hatchery-reared M. dalli produced by aquaculture-based enhancement programs.