Benthic assemblages in the fjord-like Bathurst Channel estuarine system, south-western Tasmania, vary over horizontal scales of 1–5 km and vertical scales of 1–10 m. Multivariate analysis indicated a total of eight major assemblages that characterize different sections and depths of the channel. Because tannins in the low-salinity surface water layer block light, foliose algae reach 5 m depth in the marine western region but do not penetrate below 1 m in the east. By contrast, sessile invertebrates are most abundant below 5 m depth in the west and below 2 m in the east. Deeper assemblages are unlikely to be continuous with assemblages in deeper waters off the Tasmanian coast as they are highly constrained by depth within particular sections of the estuary. While the species composition of the Bathurst Channel biota is most similar to that found elsewhere in Tasmania, the structural character of the biota in terms of major taxonomic groups is more closely allied to that found in fjords of south-western Chile and south-western New Zealand. These three regions all possess wilderness settings, high rainfall that is channelled through estuaries as a low-salinity surface layer, deep-water emergence of fauna, rapid change in biotic communities over short horizontal and vertical distances, and high levels of local endemism. They also include some of the most threatened aquatic ecosystems on earth due to increasing human activity from a near pristine base, and the potentially catastrophic impacts of climate change. Copyright © 2009 John Wiley & Sons, Ltd.