In eastern Australia, small ephemeral soft-sediment pools are common on sheltered sand- and mudflats, and are occupied by the juveniles of fishes of economic and ecological importance. To address the question of whether these pools are merely refugia or whether they constitute a hitherto unrecognised nursery feeding habitat for small obligate meiobenthivorous fishes, we surveyed the meiofaunal communities of ephemeral soft-sediment pools within three intertidal shores of Moreton Bay, Australia. Highest mean meiofaunal abundances occurred at Godwin Beach and differed significantly throughout the year. Nematodes and copepods were the most abundant taxa while all other taxa contributed to <10% of the total meiofaunal abundance. Pool characteristics (i.e. volume and surface area) did not correlate with the abundance of benthic faunal assemblages. Overall, ephemeral soft-sediment pools of Moreton Bay support meiofaunal communities that are likely to provide prey resources for juvenile and small fish that use them as nurseries at low tide.