We review the status of marine shellfish ecosystems formed primarily by bivalves in Australia, including: identifying ecosystem-forming species, assessing their historical and current extent, causes for decline and past and present management. Fourteen species of bivalves were identified as developing complex, three-dimensional reef or bed ecosystems in intertidal and subtidal areas across tropical, subtropical and temperate Australia. A dramatic decline in the extent and condition of Australia’s two most common shellfish ecosystems, developed by Saccostrea glomerata and Ostrea angasi oysters, occurred during the mid-1800s to early 1900s in concurrence with extensive harvesting for food and lime production, ecosystem modification, disease outbreaks and a decline in water quality. Out of 118 historical locations containing O. angasi-developed ecosystems, only one location still contains the ecosystem whilst only six locations are known to still contain S. glomerata-developed ecosystems out of 60 historical locations. Ecosystems developed by the introduced oyster Crasostrea gigas are likely to be increasing in extent, whilst data on the remaining 11 ecosystem-forming species are limited, preventing a detailed assessment of their current ecosystem-forming status. Our analysis identifies that current knowledge on extent, physical characteristics, biodiversity and ecosystem services of Australian shellfish ecosystems is extremely limited. Despite the limited information on shellfish ecosystems, a number of restoration projects have recently been initiated across Australia and we propose a number of existing government policies and conservation mechanisms, if enacted, would readily serve to support the future conservation and recovery of Australia’s shellfish ecosystems.

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An Australia-wide assessment of ~1000 estuaries and embayments undertaken by the National Land and Water Resources Audit of 1997–2002 indicated that ~30% were modified to some degree. The most highly degraded were in New South Wales, where ~40% were classified as ‘extensively modified’ and <10% were ‘near pristine’. Since that review, urban populations have continued to grow rapidly, and increasing pressures for industrial and agricultural development in the coastal zone have resulted in ongoing degradation of Australia's estuaries and embayments. This degradation has had serious effects on biodiversity, and commercial and recreational fishing. A business case is developed that shows that an Australia-wide investment of AU$350 million into repair will be returned in less than 5 years. This return is merely from improved productivity of commercial fisheries of a limited number of fish, shellfish and crustacean species. Estuary repair represents an outstanding return on investment, possibly far greater than most of Australia's previous environmental repair initiatives and with clearly demonstrated outcomes across the Australian food and services economies.

Documented impacts of climate change on marine systems indicate widespread changes in many geographic regions and throughout all levels of the ocean's food webs. Oceans provide the main source of animal protein for over a billion people, and contribute significantly to food security for billions more. Clearly, if we are to continue to derive these benefits, then the rate of adaptation in our human systems needs to at least keep pace with the rate of ecological change for these benefits to continue. An Australia-wide program of research into marine biodiversity and fisheries explored the opportunities for policy and management to respond to a changing climate. The research program spanned all Australian estuarine-nearshore and marine environments-tropical, subtropical, and temperate-and focused on two key marine sectors: biodiversity conservation and fisheries (commercial, recreational, and aquaculture). Key findings from across this strategic and extensive research investment were the need to foster resilience through habitat repair and protection, improve resource allocation strategies, fine-tune fisheries management systems, and enhance whole of government approaches and policies. Building on these findings, from a climate adaptation perspective, we generated a checklist of thirteen elements encompassing all project findings to assess and steer progress towards improving marine policy and management. These elements are grouped in three broad areas: preconditioning; future proofing; and transformational changes and opportunities. Arising from these elements is a suite of priority strategies that provide guidance for marine managers, policy practitioners, and stakeholders as they prepare for a future under climate change. As the research program encompassed a wide range of habitats and ecosystems, spanned a latitudinal range of over 30°, and considered a diversity of management systems and approaches, many of these elements and strategies will be applicable in a global context.

Managers are moving toward implementing large-scale coastal ecosystem restoration projects, however, many fail to achieve desired outcomes. Among the key reasons for this is the lack of integration with a whole-of-catchment approach, the scale of the project (temporal, spatial), the requirement for ongoing costs for maintenance, the lack of clear objectives, a focus on threats rather than services/values, funding cycles, engagement or change in stakeholders, and prioritization of project sites. Here we critically assess the outcomes of activities in three coastal wetland complexes positioned along the catchments of the Great Barrier Reef (GBR) lagoon, Australia, that have been subjected to restoration investment over a number of decades. Each floodplain has been modified by intensive agricultural production, heavy industry and mining infrastructure, urban/peri urban expansion, aquaculture development and infrastructure expansion. Most development has occurred in low-lying coastal floodplains, resulting in major hydrological modifications to the landscape. This has left the floodplain wetlands in a degraded and hydrologically modified state, with poor water quality (hypoxic, eutrophication, sedimentation, and persistent turbidity), loss of habitat, and disconnected because of flow hydraulic barriers, excessive aquatic plant growth, or establishment of invasive species. Successful GBR wetland ecosystem restoration and management first requires an understanding of what constitutes "success" and must be underpinned by an understanding of complex cause and effect pathways, with a focus on management of services and values. This approach should recognize that these wetlands are still assets in a modified landscape. Suitable, long term, scientific knowledge is necessary to provide government and private companies with the confidence and comfort that their investment delivers dividend (environmental) returns.