The Marine chapter of the 2016 State of the Environment (SoE) report incorporates multiple expert templates developed from streams of marine data. This metadata record describes the Case Study "Commonwealth commercial fisheries". The full Case Study, including figures and tables (where provided), is attached to this record. Where available, the Data Stream(s) used to generate this Case Study are accessible through the "On-line Resources" section of this record. DESCRIPTION OF THE FOCUS OF THE CASE STUDY Management of commercial fisheries is shared between the Commonwealth, states and the Northern Territory. In general, the Australian Government, through the Australian Fisheries Management Authority (AFMA), is responsible for commercial fishing beyond three nautical miles from the coast. Some Commonwealth fisheries target fish stocks that extend into the high seas and the Exclusive Economic Zones of other countries. These are jointly managed with other countries through conventions and agreements. Key commercial stocks in Commonwealth fisheries are managed under the Commonwealth Fisheries Harvest Strategy Policy (HSP). The HSP requires an evidence–based approach to setting sustainable catch levels to ensure stocks are maintained at ecologically sustainable levels and within this context, maximise economic returns to the Australian community. The Australian Government aims to implement an ecosystem-based approach to fisheries management, which considers fisheries’ interactions with, and impacts on, bycatch species, habitats, communities and ecosystems. Bycatch species are managed under the Commonwealth Policy on Fisheries Bycatch (BCP) and in line with Environment Protection and Biodiversity Conservation Act 1999 (EPBC Act) requirements. The BCP aims to reduce bycatch and improve protection for vulnerable species; this is implemented through a risk management framework. PRESSURES/ISSUES OF IMPORTANCE The 2013 HSP review found the policy and guidelines improved the management of Commonwealth fisheries. The HSP is one of only a few comprehensive policies implemented to direct the development of harvest strategies across fisheries. DATA STREAM(S) USED IN CASE STUDY Fishery status reports data, 1992 to 2014 covering all Commonwealth fisheries (as described in Patterson et al 2015). The status assessments are underpinned by AFMA’s fishery catch and effort data and the data used in individual fish stock assessments.

The Marine chapter of the 2016 State of the Environment (SoE) report incorporates multiple expert templates developed from streams of marine data. This metadata record describes the Case Study "Pressures on the marine environment associated with shipping". The full Case Study, including figures and tables (where provided), is attached to this record. Where available, the Data Stream(s) used to generate this Case Study are accessible through the "On-line Resources" section of this record. DESCRIPTION OF THE FOCUS OF THE CASE STUDY Australia as an island relies heavily on shipping for transportation of its imports and exports. In 2013–14, approximately 1274 million tonnes of cargo were loaded and 151 million tonnes discharged at Australian wharves by 5499 vessels that made 28 714 port calls (BITRE 2015). As this shipping traverses Australian waters there is potential for adverse interactions with the marine environment across all regions (see Figure 1 in full case study attached). PRESSURES/ISSUES OF IMPORTANCE There is a risk of environmental damage from collision or grounding of vessels, and ship strike, which is a significant cause of anthropogenic mortality to whales worldwide. In addition, small recreational vessels regularly injure dugongs, turtles, and dolphins. Known Australian ship strike incidents in recent times have predominately involved humpback whales and based on behaviour and distribution there is potential for mother-calf pairs to be particularly susceptible. There have also been reported incidents with southern right whales, sperm whales and pygmy blue whales. Given the speed and size of modern shipping, collisions with whales have a high probability of being fatal. DATA STREAM(S) USED IN CASE STUDY Ship strike reports derived from the Australian Marine Mammal Centre National Marine Mammal Database, Vessel tracking data (AIS records).

The Marine chapter of the 2016 State of the Environment (SoE) report incorporates multiple expert templates developed from streams of marine data. This metadata record describes the Case Study "National Marine Science Plan". The full Case Study, including figures and tables (where provided), is attached to this record. Where available, the Data Stream(s) used to generate this Case Study are accessible through the "On-line Resources" section of this record. DESCRIPTION OF THE FOCUS OF THE CASE STUDY The National Marine Science Plan (the Plan) is a decadal plan designed to focus investment on the biggest development and sustainability challenges facing Australia's marine estate, and the highest priority science needed to tackle these challenges to fulfill our blue economy’s potential. The grand challenges are highly relevant to the State of Australia's Marine Environment, including energy security; food security; biodiversity conservation and ecosystem health; urban coastal environments; climate variability and change; and resource allocation. The Plan was developed under the auspices of the National Marine Science Committee (NMSC), on which senior representatives of 23 research institutions, universities and government departments work together to plan, coordinate and communicate marine science and its application to national priorities. Over 500 marine scientists and stakeholders took part in the development of the Plan, beginning with the development of eight community white papers. The white paper process involved stakeholders from the different marine science sectors working to identify the science required to address grand challenges. The white papers were presented and discussed at a National Marine Science Symposium in November 2014, followed by two further rounds of consultation. The finalised Plan brings together the highest priority science and science capabilities (skills, infrastructure and relationships) to meet a cross-section of challenges areas in an integrated and strategic manner. ISSUES OF IMPORTANCE To focus the coordination efforts and investments, the Plan sets out eight high level recommendations. Create an explicit focus on the blue economy throughout the marine science system. Establish and support a National Marine Baselines and Long-term Monitoring Program to develop a comprehensive assessment of our estate, and to help manage Commonwealth and State Marine Reserve networks. Facilitate coordinated national studies on marine ecosystem processes and resilience to enable understanding of the impacts of development (urban, industrial and agricultural) and climate change on our marine estate. Create a National Oceanographic Modelling System to supply defence, industry and government with accurate, detailed knowledge and predictions of ocean state to support decision-making by policymakers and marine industry. Develop a dedicated and coordinated science program to support decision-making by policymakers and marine industry. Sustain and expand the Integrated Marine Observing System to support critical climate change and coastal systems research, including coverage of key estuarine systems. Develop marine science research training that is more quantitative, cross-disciplinary and congruent with industry and government needs. Fund national research vessels for full use. All of these recommendations will improve the national capacity to provide evidence-based assessments on the state of Australia’s vast and valuable marine environment. DATA STREAM(S) USED IN CASE STUDY Synopsis of the National Marine Science Plan.

The Marine chapter of the 2016 State of the Environment (SoE) report incorporates multiple expert templates developed from streams of marine data. This metadata record describes the Case Study "traditional management of marine resources in Torres Strait". The full Case Study, including figures and tables (where provided), is attached to this record. Where available, the Data Stream(s) used to generate this Case Study are accessible through the "On-line Resources" section of this record. DESCRIPTION OF THE FOCUS OF THE CASE STUDY The Torres Strait region is renowned for its ecological complexity and biodiversity, providing a multitude of habitats and niches for the highly diverse Indo-Pacific marine flora and fauna, including dugongs and marine turtles. The Torres Strait is of enormous significance from an Indigenous cultural resource management perspective. Marine and island resources traditionally have been, and continue to be, vital to Torres Strait Islanders from a subsistence and cultural viewpoint. Torres Strait Islanders have a strong and abiding connection with their islands and sea country, governed by the unique Ailan Kastom (Island Custom). DATA STREAM(S) USED IN CASE STUDY Relevant peer review publications and reports. Case study based on literature review.

The Marine chapter of the 2016 State of the Environment (SoE) report incorporates multiple expert templates developed from streams of marine data. This metadata record describes the Expert Assessment "The state and trends of ecological processes – trophic structures and relationships". The full Expert Assessment, including figures and tables (where provided), is attached to this record. Where available, the Data Stream(s) used to generate this Expert Assessment are accessible through the "On-line Resources" section of this record. DESCRIPTION OF ECOLOGICAL PROCESS FOR EXPERT ASSESSMENT For this assessment, food web structure and function as defined by diet and modelling studies (which synthesis much of the available information) have been used to evaluate the status and trends for trophic structures and relationships. The status and outlook for the structure of Australian marine ecosystems is highly variable. Food webs are naturally dynamic, through time and space (e.g. Griffiths et al. 2009), and human pressure on them has varied around Australia over the past two centuries, altering trophic structures to differing degrees (Dell et al. 2013, GBRMPA 2014). Food webs studies have primarily focused on coastal and shelf waters (e.g. Salini et al 1998, Bulman et al. 2001, DofWWA 2009), with much less coverage of deep water food webs. Diet studies have only occurred intermittently and few studies have been subsequently repeated (e.g. recent resampling of fish diets on the shelf of SE Australia; CSIRO unpublished). Consequently, understanding the true magnitude of inter-annual variation in diets is low and there is little capacity to be sure of dietary changes through time. Modelling studies (Fulton et al. 2005, Klaer 2005) suggest there has been trophic restructuring of food webs in south-eastern Australia over the last century, particularly as a result of the intensification of commercial fisheries up to the 1990s. The reduction in fishing pressure, particularly over the last 5-10 years (Flood et al. 2014, Patterson et al. 2015) will likely, eventually, allow the recovery of trophic structures. However, a complete recovery is unlikely given the multitude of on-going pressures (e.g. remaining fishing pressure, both recreational and commercial, shipping, coastal habitat modification, pollution, etc.) and because some highly depleted species (e.g. eastern gemfish) have failed to recover from past overexploitation; which itself may be related to shifts in trophic connections with predators and prey (TSSC 2009). In addition, climate change is reshaping south eastern ecosystems, with shifts in species ranges (Sunday et al. 2015) and the realisation of new trophic interactions (e.g. shifts in octopus diets; Briceno et al. 2015), as omnivorous species appear to shift more rapidly than carnivores (Sunday et al. 2015). Eastern Australian ecosystems, including the Great Barrier Reef are highly modified (Butler and Jernakoff 1999, GBRMPA 2014). Amongst the most obviously shifted systems are around population centres and in the southern Great Barrier Reef (GBRMPA 2014). As elsewhere, fishing pressure has eased over the past 5 years, but other pressures (e.g. from increasing development) have increased (AIMS 2014). Overall trophic structures likely remain highly modified, both by past and present removal of predatory species and shifts in abundance of basal species, due to eutrophication or habitat removal (GBRMPA 2014, Fulton and Gorton 2014). The ecosystems of northern, western, southwestern and southern Australia see less direct, and spatially more variable, pressure than those in the east and south east. Over the past 3 decades, fishing pressure in the region has significantly declined, and has continued to do so (though at a reduced rate) over the past 5 years (Prince et al. 2008, Patterson et al. 2014, Fletcher and Santoro 2015). Development of other sectors (e.g. shipping) has grown, but largely concentrated on specific locations (AIMS

The Marine chapter of the 2016 State of the Environment (SoE) report incorporates multiple expert templates developed from streams of marine data. This metadata record describes the Expert Assessment "Effectiveness of marine management of commercial fishing". The full Expert Assessment, including figures and tables (where provided), is attached to this record. Where available, the Data Stream(s) used to generate this Expert Assessment are accessible through the "On-line Resources" section of this record. DESCRIPTION OF THE PRESSURE BEING MANAGED, AND ITS IMPACT Ecologically Sustainable Development (ESD) is a common objective across all Australian jurisdictions resulting in a good level of understanding of the direct pressures commercial fishing has on the marine environment. All Australian jurisdictions have introduced one or more measures to address those pressures that are increasingly based on risk assessment and implementing a management response. These include harvest strategies for the main commercial species, adaptive management involving expert judgement, more quantitative management strategy evaluation, ecosystem modelling and broader ecological risk assessments. There is now a greater understanding of the effects of climate change and ocean acidification on the marine environment and the need to consider this when determining appropriate fisheries management responses. However, management agencies are yet to integrate all the available science into their management systems. Likewise, current habitat analysis work will identify the emerging priorities in managing the environmental effects on habitats of commercial fishing. Spatial management has been introduced to mitigate the impacts on both vulnerable species and habitats where identified i.e. gulper shark closures in the Southern and Eastern Scalefish and Shark Fishery and the introduction of gillnet zoning closures to limit interactions with the Australian sea lion. Similarly, spatial closures that specifically prohibit trawling within seagrass and other sensitive nursery habitats are often used for many fisheries including, for example, the Shark Bay and Exmouth Gulf prawn trawl fisheries in Western Australia. Specific mitigation measures for protected species are also used to reduce the effects of commercial fishing. This includes such things as: seal and turtle excluder devices, square mesh panels in trawls, tori lines and other sea bird deterrent devices. Education programs for the fishing industry have also been improved to provide a greater understanding of how to avoid and/or handle protected species. DATA STREAM(S) USED IN EXPERT ASSESSMENT The assessment is based on relevant literature and reports on current management measures associated with commercial fishing – a list is provided in the attached Expert Assessment. 2016 SOE ASSESSMENT SUMMARY [see attached Expert Assessment for full details] • Understanding of pressure: Understanding of fisheries and effective management frameworks is reasonably high and improving. • Planning associated with management of pressure: Improved planning processes directed towards research and risk-based assessment processes are resulting in more robust outcomes. • Input for informing management of pressure: Greater use of technology for data collection informs management decisions and measures the trajectory of trends over time. • Processes associated with developing, monitoring, and updating management: Improved processes have been developed to expand the range of fishery assessment tools with an increased use of risk-based approaches. • Outputs from management framework in place: Biennial State of key Australian Fish Stocks Report form the primary assessment output for national commercial fisheries. • Outcomes of management framework in place: Improvements in data gathering and reporting direct resources towards commercial fishing operations that pose the highest risk to the marine environment. CHANGES SINCE 2011 SOE

The Marine chapter of the 2021 State of the Environment (SoE) report incorporates multiple expert templates developed from streams of marine data. This metadata record describes the Case Study "Lessons for marine management derived from fisheries management practices". A PDF of the full Case Study, including figures and tables (where provided) is downloadable in the "On-line Resources" section of this record as "CASE STUDY 2021 – Lessons for marine management derived from fisheries management practices" DESCRIPTION OF FOCUS FOR THE CASE STUDY This case study summarises key lessons from Australian fisheries management that are relevant to the management of natural marine, freshwater and terrestrial environments and resources more broadly and highlight opportunities for improved natural resource management. For example, Australian fisheries management has used innovative approaches to (i) reduce conflict in decision-making with defined targets and reference points (e.g. as part of harvest strategies), (ii) explore consequences of implementing different management decisions in fisheries systems (e.g. management strategy evaluation), (iii) apply the precautionary principle (e.g. ecological risk assessments), and (iv) consider a wider range and cumulative impacts, including climate change, on marine systems. The success of the arrangements is due to co-development with expertise-based consultative forums (e.g. Resource Advisory Groups, Management Advisory Committees) where the outputs and details of these approaches are considered, questioned and agreed in a transparent and collaborative manner. DATA STREAM(S) USED IN CASE STUDY Synthesis of literature published, and expert knowledge of the case study authors.

The Marine chapter of the 2016 State of the Environment (SoE) report incorporates multiple expert templates developed from streams of marine data. This metadata record describes the Case Study "Pressures on the marine environment associated with marine debris". The full Case Study, including figures and tables (where provided), is attached to this record. Where available, the Data Stream(s) used to generate this Case Study are accessible through the "On-line Resources" section of this record. DESCRIPTION OF THE FOCUS OF THE CASE STUDY Marine debris is recognized as a globally important stressor in the marine environment, with increasing reports of impacts on marine biodiversity reported during the last four decades and upwards of 6-12 million metric tons of plastic waste entering the oceans each year. However, this pressure was not included in the 2011 assessment, but was identified as an emerging issue in the previous SoE report. Marine litter includes consumer items such as glass or plastic bottles, cans, bags, balloons, rubber, metal, fiberglass, cigarettes and other manufactured materials that end up in the ocean and along the coast, and other materials intentionally or unintentionally discarded at sea. In Australia, marine debris has been identified as a key threatening process for threatened and endangered vertebrate fauna, with approximately ¾ of items found on beaches being comprised of plastic polymers. Marine litter also has socioeconomic impacts, it acts as a transporter of invasive species, can be a navigation hazard and there are increasing concerns over the human health risks due to food security issues from seafood. With estimates of ¾ or more of marine debris coming from land-based sources and continued growth in plastics production and usage, marine debris is a ubiquitous problem, with high but variable concentrations of marine debris found both in coastal and marine environments. PRESSURES/ISSUES OF IMPORTANCE Marine fauna as small as plankton and as large as cetaceans are known interact with marine debris; with entanglement, ingestion and chemical contamination the three main types of interaction. Corals, lugworms, molluscs, commercial fish, seabirds sea turtles, sea snakes, pinnipeds, whales and dolphins are all reported to be impacted by marine debris, with significant quantities of plastics reported in the digestive tracts of several species of marine vertebrates in Australian waters. DATA STREAM(S) USED IN CASE STUDY Concentrations [of marine debris] derived from a single survey around Australian coastline and at sea, carried out between 2011-2013 as well as data and analyses presented in peer review publications, a recent review of the TAP for marine debris.

The Marine chapter of the 2016 State of the Environment (SoE) report incorporates multiple expert templates developed from streams of marine data. This metadata record describes the Expert Assessment "The state and trends of quality of species and groups – Epipelagic fish species". The full Expert Assessment, including figures and tables (where provided), is attached to this record. Where available, the Data Stream(s) used to generate this Expert Assessment are accessible through the "On-line Resources" section of this record. DESCRIPTION OF ECOLOGICAL SPECIES/COMMUNITY FOR EXPERT ASSESSMENT Australia’s coastal small pelagic fishes (<50 cm) include species such as Australian Sardines, Maray, Blue and Sandy Sprats, Australian anchovy, scads, Jack Mackerel, hardyheads, silversides, Blue mackerel, Australian Herring and Redbait. Tropical and temperate assemblages are comprised of different species and there are also regional differences in species composition (Hobday et al. 2009). This assessment refers only to temperate species in the East, South-east and South-west regions. Blue Mackerel, Common Jack Mackerel, Redbait and Australian Sardine (off eastern Australia only) are targeted by the Commonwealth Small Pelagic Fishery. The SPF is managed in two Zones: East spanning half of the East and eastern South-east regions and the West spanning the South west and western half of South-east). State fisheries primarily target Australian Sardine but may also take Australian Anchovy, Blue Mackerel, sprats and Maray. DATA STREAM(S) USED IN EXPERT ASSESSMENT The assessment is based on data and analyses published in the peer review literature, stock assessment reports and minutes of the meetings of the Small Pelagic Fishery Scientific Panel. Details of specific data sets used to generate the assessment have not been provided. 2016 SOE ASSESSMENT SUMMARY [see attached Expert Assessment for full details] • 2016 • Assessment grade: Good Assessment trend: Stable Confidence grade: Adequate high quality evidence and high level of consensus Confidence trend: Adequate high quality evidence and high level of consensus Comparability: Grade and trend are comparable to the 2011 assessment • 2011 • Assessment grade: Good Assessment trend: Stable Confidence grade: Adequate high quality evidence and high level of consensus Confidence trend: Limited evidence or limited consensus CHANGES SINCE 2011 SOE ASSESSMENT Additional fishery catch data, more recent stock assessments.

The Marine chapter of the 2016 State of the Environment (SoE) report incorporates multiple expert templates developed from streams of marine data. This metadata record describes the Case Study "The National assessment of shallow reefs". The full Case Study, including figures and tables (where provided), is attached to this record. Where available, the Data Stream(s) used to generate this Case Study are accessible through the "On-line Resources" section of this record. DESCRIPTION OF THE FOCUS OF THE CASE STUDY Shallow rocky and coral reef biodiversity (<25 m depth) around Australia’s coasts and at offshore islands and reef systems. This assessment is based on the recent Australia-wide rollout of Reef Life Survey monitoring methodology (data available at http://reeflifesurvey.imas.utas.edu.au), which includes consideration of reef fishes, large mobile invertebrates such as sea urchins, crown of thorns, lobsters and abalone, and habitat-forming seaweeds and corals. PRESSURES/ISSUES OF IMPORTANCE Pressures from recreational and commercial fisheries are of particular importance to larger fish species and lobsters, while ocean warming is having widespread impacts on the composition of communities in temperate zones. The marine heatwave in WA has had a particularly large impact on shallow water reef biodiversity in WA since SoE 2011, with widespread coral bleaching in the northwest and loss of kelp habitats and changing fish communities in the southwest. Cyclones and storms have also had substantial impacts on coral communities at Ningaloo Reef and parts of the GBR. Inner Great Barrier Reef coral structures have been adversely affected by siltation and nutrification. DATA STREAM(S) USED IN CASE STUDY Reef Life Survey visual census data were used for the current status assessment, with extensive spatial coverage of sites around the continent. Temporal trend information came from a combination of RLS, LTTRMP and AIMS long-term GBR monitoring datasets at 16 particular locations (MPA locations include the broader region and sites inside and outside sanctuary zones): NSW: Batemans Marine Park, Jervis Bay Marine Park, Sydney, Lord Howe Island, Port Stephens VIC: Beware Reef, Port Phillip Heads SA: Encounter Bay (Fleurieu Peninsula) WA: Rottnest Island, Jurien Marine Park, Ningaloo Marine Park QLD: Capricorn-Bunker, Southern GBR, Central GBR, Northern GBR TAS: Maria Island