The marine reserve at inner Doubtful Sound, Taipari Roa, covers an area of about 613 hectares and was one of eight marine reserves established in 2005 as part of the management measures proposed by the Guardians of Fiordland.
The reserve contains extensive rock wall habitat on the western side of Elizabeth Island and deep kelp beds on the southern end of the island. In the channel between Elizabeth Island and the eastern side of the fiord there is a relatively shallow channel which experiences high water flow and is home to a range of suspension feeders including black and red coral and zooanthids. While the south-eastern wall of the reserve is heavily shaded, many of the other coastlines receive moderate amounts of direct sunlight in the summer months.
The construction of the Manapōuri Hydroelectric power scheme in 1969 caused major modifications to the hydrographic environment in Doubtful Sound. This scheme involved the construction of a tailrace tunnel from Lake Manapōuri to Deep Cove and resulted in more than three times more freshwater than previously coming into to Doubtful/Thompson Sound. Monitoring of the area suggests that there have been some major changes in marine communities in Doubtful Sound as a result, including effects on black corals around Elizabeth Island.
The reserve is often visited by a well-studied population of bottlenose dolphins, and Rolla Island is known as a site for Fiordland crested penguins. The reserve is also home to a unique assemblage of bright yellow glass sponges that have only ever been seen elsewhere in caves in Jamaica.