Coastal lagoons of the principal islands of Bass Strait, between Australia's mainland and Tasmania, were sampled in two summers. Many, particularly those of low to moderate salinity, contain relatively rich assemblages of microinvertebrates and some endemic Australian freshwater algae. Several species of testate amoebae and rotifers could not be referred to known morphotypes and are probably new species. The presence of certain species on islands of Bass Strait provides a link between populations in mainland Australia and others in Tasmania. Those lagoons are identified that, by virtue of catchments or buffer zones clothed in native vegetation, are favourable for the survival of a native and partly endemic microbiota.