The NWS-InVitro model is a spatially explicit agent-based biophysical simulation model with adaptive time-steps and asynchronous submodel execution. It has been developed as the basis of the NWS-JEMS management strategy evaluation study. The model simulates a range of human activity and principal features of the marine ecosystem in Australia's North West Shelf (NWS) region under a variety of management strategies. The results of the simulations are to be used to assess the relative efficacy and robustness of these strategies across a broad range of environmental and economic conditions. NWS-InVitro takes a wide range of environmental/ecosystem data and data concerning human activity as input. Data typically used to configure the ecosystem and its environment would include bathymetry, rainfall, current fields, contaminant fields, wind, and the distribution and abundance of organisms simulated as well as the usual biological parameters such as mortality and growth rates. Data relating to human activity may include control zones for vessel movement or fishing, historical catch, locations of artefacts (platforms, ports, pipelines, etc), and population time series for ports, though it is not limited to these data. Data which is characteristically produced in a simulation includes distribution and abundance of simulated species, catch/cpue history, vessel movement and conflicts, contamination effects, and a range of other data. There is a degree of randomness in some of the process models used to represent the behaviour of components of the simulation, so the output data will differ between runs. These output data sets are meant to be used as a part of large number of runs which encompasses the likely variability in the modelled systems. A typical suite of runs will run to over a half a TByte. See References for information regarding the specific configurations used with respect to parameterisation, input and output data.

The region of interest for this study was Australias North West Shelf, extending from the inter-tidal zone to the continental shelf break, with particular focus on data relevant to the area between North West Cape and Port Hedland. The principal resource used for identification of existing data and information was the bibliography assembled by Jernakoff et al. (2006). This document provides an overview of the relevance of existing information to the North West Shelf Marine Environmental Management Study (NWSMEMS). It identifies gaps in knowledge that are likely to be important to the NWSMEMS and makes recommendations for addressing these gaps. The review presents information on the marine environment, grouped into physical, chemical and biological themes. This summary at the beginning of the document presents our major conclusions about the relevance of existing knowledge and about major gaps in information, and our recommendations for future research.

The West Australia Department of Environmental Protection (DEP) initiated a North West Shelf (NWS) Marine Environmental Management Study in 1998 to develop and consolidate the technical information base, scientific understanding and predictive capabilities required to underpin environmental decision making in both the public and private sectors. Documents, reports and scientific publications pertinent to the North West Shelf are abundant, but vary widely in scope and the degree of relevance to environmental management. Much of the information is from industries and associated government departments involved in exploiting and managing resources, and much of it has been activity specific and/or site specific in nature. This has created rich pockets of specialist knowledge but, unfortunately, the information has not been integrated across industries, government departments or scientific disciplines. Such integration is attractive, but difficult to achieve. As an example, the petroleum industry initiated its own review in the early 1990s to coordinate the then state of knowledge among its members, but has recently identified the need to revisit the process. As a first step in the North West Shelf Marine Environmental Management Study, DEP commissioned the Australian Institute of Marine Science (AIMS) and the Commonwealth Scientific and Industrial Research Organisation (CSIRO) Division of Marine Research to conduct a compilation and review of scientific research and data related to the North West Shelf marine environment. This bibliography is one product of that effort; it provides a compilation of published and unpublished literature generally related to the North West Shelf marine environment and its management. The second product, a review of scientific research and identification of important knowledge gaps, appears as a separate report by Heyward, Revill, and Sherwood (2006), titled Review of Research and Data Relevant to Marine Environmental Management of Australias North West Shelf.

The West Australia Department of Environmental Protection (DEP) initiated a North West Shelf (NWS) Marine Environmental Management Study in 1998 to develop and consolidate the technical information base, scientific understanding and predictive capabilities required to underpin environmental decision making in both the public and private sectors. Documents, reports and scientific publications pertinent to the North West Shelf are abundant, but vary widely in scope and the degree of relevance to environmental management. Much of the information is from industries and associated government departments involved in exploiting and managing resources, and much of it has been activity specific and/or site specific in nature. This has created rich pockets of specialist knowledge but, unfortunately, the information has not been integrated across industries, government departments or scientific disciplines. Such integration is attractive, but difficult to achieve. As an example, the petroleum industry initiated its own review in the early 1990s to coordinate the then state of knowledge among its members, but has recently identified the need to revisit the process. As a first step in the North West Shelf Marine Environmental Management Study, DEP commissioned the Australian Institute of Marine Science (AIMS) and the Commonwealth Scientific and Industrial Research Organisation (CSIRO) Division of Marine Research to conduct a compilation and review of scientific research and data related to the North West Shelf marine environment. This bibliography is one product of that effort; it provides a compilation of published and unpublished literature generally related to the North West Shelf marine environment and its management. The second product, a review of scientific research and identification of important knowledge gaps, appears as a separate report by Heyward, Revill, and Sherwood (2006), titled Review of Research and Data Relevant to Marine Environmental Management of Australias North West Shelf.

Specific objectives of the contaminants component of the North West Shelf Joint Environmental Management Study were to: Establish an inventory of contaminant inputs (nutrients and toxicants) from all known point and diffuse sources; Review the pathways, fates and bioavailability of the contaminants of concern in the water, sediments and biota; Establish environmental quality criteria to assess environmental health and provide early indications of environmental degradation; and For the contaminants of concern, collate and evaluate the applicability of available toxicological data, and if necessary develop acute and chronic toxicity data using local marine indicator species. The North West Shelf (NWS) has been subject to inputs of contaminants (toxicants and nutrients) from a variety of point and diffuse sources over the last 35 years. The various types of contaminants behave differently and can have different effects depending on their loads to, and concentrations in, the environment. Effective environmental management relies on an understanding of the types and quantities of wastes discharged, the sources of those discharges and their environmental consequences viewed individually and from a cumulative perspective, and considering both acute and chronic effects. An electronic database of annual loadings of point source contaminants discharged into NWS waters has been compiled for the period 1985 to 2001. The contaminants include toxicants such as heavy metals and petroleum compounds and nutrients such as nitrogen. Concentrations of heavy metals in the waters surrounding the offshore petroleum facilities were lower than the highest level of protection specified in the ANZECC & ARMCANZ (2000) guidelines. There are significant discharges of heavy metals from the Parker Point Power Station where the annual loads in 2000 range from 252 kg/yr for cadmium to 8 145 kg/yr for zinc. There appears to be no data on the concentration levels of these metals in the waters or the sediments surrounding the discharge sites. In 2000, 12 million tonnes of produced formation water containing 214 tonnes of oil was discharged from nine offshore petroleum facilities. This compares with an estimated 3,300 tonnes of oil naturally seeping into NWS waters. Few studies of the fates and effects of petroleum-based compounds have been undertaken on the NWS. These studies report no acute effects, but suggest that chronic and sub-lethal effects on marine plankton and bacteria have occurred in the vicinity of some of the production platforms. Concentrations of the antifouling chemical, tributyltin (TBT), were found in coastal waters of the Dampier Archipelago to be at levels ranging from 0.003 to 0.025 μg/L. In chapter 3 we review what is known about fates, pathways and potential bioavailability for the key contaminants of concern identified as part of the contaminants inventory and the review of toxicological data (chapter 4). These contaminants were identified as: six metals; barium, cadmium, chromium, copper, lead, mercury and zinc; one organometalloid: tributyltin (TBT); one nutrient: nitrogen; a waste stream; produced formation waters (PFW); and hydrocarbons (oil). The results of the water quality study indicate that the coastal waters of the North West Shelf are generally of very high quality. The concentrations of metals were low by world standards, with localised elevations of some metals adjacent to industrial centres and ports. No organic chemicals were detected. The reporting limits were well below the guideline trigger values recommended in ANZECC & ARMCANZ (2000) for a very high level of ecological protection for the five organics for which guideline values were available. The findings of this study suggest that ANZECC & ARMCANZ (2000) 99% species protection guidelines are relevant to the region for all metals analysed, except cobalt, for which the 95% species protection guideline is recommended for u

The overall aims were to provide data on the distribution of deep seabed habitats and fauna that are amenable to scientific hypothesis testing, can be immediately applied to marine resource management processes, and that enable strategic development of tools and techniques for understanding the processes that maintain deep sea biodiversity. This work was to support the process of NWR Estate inventory and management performance assessment by providing interpreted benthic habitat maps, faunal inventories, distribution maps and conservation values. Data will be collected at scientific reference sites from potential MPA areas that can be re-visited for monitoring purposes in the future. Sampling along environmental gradients (geographic range and depth) in this section of Australia's coast will also provide the opportunity to evaluate biogeographic hypotheses. Further refinement of predictive methods for identifying seabed habitat types, initially developed in temperate and cool-temperate environments, will be enabled by data collection from this tropical location in Australia. We intended to highlight the importance of this underlying science as a modern "Voyage of Discovery" given the likely significance of the findings in terms of Australia's biodiversity and its biogeography and evolution. (From Voyage Plan) This record describes the biological samples taken during the survey. Fishes were lodges in the CSIRO Fish collection, invertebrate specimens were photographed and distributed to Australian museums for identification by taxonomists, focusing on sponges, corals, echinoderms, ascidians, molluscs and crustaceans. To date (as per Dec 2016) we are aware of 27 manuscripts of taxonomic revisions and/or descriptions that have used material collected from this survey.

Relevant spatial datasets for mapping pressures were identified and collated. Pressures were categorised as resource extraction and use, pollution, habitat modification, climate, and ‘other’. Pressures included Commonwealth trawl fisheries effort, aquaculture infrastructure, location of oil and gas infrastructure, historical shipping and pollution data, location of historical seismic operations, cyclone intensity, spoil dumping, sewage outfalls, location of ports, and tourism operations. Two main pressure maps were derived i) an additive pressure hotspots map, which gives higher weight to areas with multiple pressures of high risk; and, ii) a multiplicative hotspot pressure map, which gives lower weighting to areas with multiple low risk pressures. Areas of high risk were identified, and thus possibly high benefit for management versus low risk or low associated benefit for mitigation. The information generated needs to be considered alongside robust species distribution data and interaction matrices for effective decision-making.

Habitats serve a variety of functions on the North West Shelf (NWS). They support the life history stages of a diverse suite of tropical species including commercially harvested ones. In addition to natural disturbance regimes, habitats are altered in response to the sectoral uses, which in turn affects the distribution and life histories of species. Habitats thus serve as the nexus linking species with uses and natural disturbance, and different habitats serve different purposes at various stages of the life history of a species. A detailed understanding of habitats, at least at the structural level, is thus a prerequisite for a more comprehensive understanding of ecological structure and functions on the North West Shelf. This component of the North West Shelf Joint Environmental Management Study (NWSJEMS) aimed to collate and integrate data on habitats for the region of the North West Shelf extending from North West Cape to Port Hedland and from the coast to the 200 m isobath. The three main activities of the study were: Development of an integrated collection of information on habitats of the North West Shelf, including expert information; Application of the CSIRO Habitat Classification Framework to the data to determine the spatial nesting and structuring of habitat units on the North West Shelf; and Provision of the habitat structure classification for input into other models developed within NWSJEMS. This record describes data of key benthic marine ecosystems and habitats. These maps and descriptions of their component attributes were designed to assist the process modelling of the ecosystem and impacts of uses, as well as directly supporting planning and management by Western Australian agencies and industries.

Data associated with outputs from the final report of the NESP MBH A12 report "Distribution and habitat suitability of Threatened and Migratory Marine Species in Northern Australia". The North Marine Bioregion is home to a diversity of threatened and data-poor marine species. In the absence of critical data on species’ distributions, population connectivity, and essential habitat, decision-making to progress the current ‘Developing the North’ agenda has the potential to negatively impact Matters of National Environmental Significance. Data compiled across multiple sources were used to model and map the distribution of 16 priority Threatened and Migratory marine species. The objective of the project was to improve the current data-poor species distribution maps held by DAWE to assist with policy decisions for these species. We used a spatial distribution modelling approach based on presence data for these species from 121 spatial datasets and associated, remotely sensed environmental variables. The output is a series of distribution maps to enhance decision-makers’ ability to assess potential impacts of development proposals in Northern Australia under the EPBC Act.