Estuaries worldwide are under increasing threat from human impacts. Because much of their fauna remains unstudied and in many cases undescribed, these systems present real challenges for effective management. In eastern Australia the study of estuarine fauna is often further complicated by its patchy distributions. This is particularly the case for assemblages of sessile invertebrates in coastal saline lakes. This study quantified distributions of sponges and ascidians at a hierarchy of spatial scales in the seagrass meadows of 2 coastal saline lakes in New South Wales, Australia. Nine species of sponge, many of which were undescribed, and 3 species of ascidians were found. Nested analyses of variance were used to identify spatial scales at which variation was significant. Most sponges and ascidians were very patchily distributed at a range of spatial scales from 10s of metres up to 100s of kilometres. The composition of assemblages differed greatly between the 2 lakes. In addition, unlike other published examples of cost–benefit analyses, in the present study very few taxa were widespread over the larger spatial scales. Cost–benefit analyses done to determine the optimal sampling design for future experiments revealed inclusion of patchily distributed taxa in analyses could improve the overall precision of sampling.