Kinorhynchs are usually collected from soft bottom and sandy sediments, whereas their occurrence in sea-grass beds rarely has been explored. In the present study we developed two new collecting methods that can recover specimens from amongst sub-tidal sea-grass beds and mangrove mud. Several species of kinorhynchs were found and one could be identified as Echinoderes teretis Brown, 1985. The species was originally found in silty mud and described from localities in Sydney Harbour and Broken Bay. We recorded the species in the Clyde River Estuary and Candlagan Creek, some 250 km further south, and in sub-tidal mud and tidal mud, also in Lake Wellington in the Gippsland Lakes, Victoria. The presence of E. teretis and several unidentifiable kinorhynch species in sea-grass beds and mangrove vegetation indicates that the provided collecting methods can reveal new information about kinorhynch diversity in such habitats.