The degradation of the Townsville coast and coastal waters of the Great Barrier Reef Marine Park ecosystem is severe. It involves, among several other symptoms, a large dam that traps riverine sand, land reclamation, extensive dredging, dumping of 400,000 m3/year of unconsolidated mud in coastal water, severe coastal erosion, sandy beaches turning muddy, healthy coral reefs turning to coral rubble, the decrease of water clarity of waters by 87 % since the 1960s, and a decrease of 80 % of the dugong population from 2016 to 2022. It is shown that this degradation is largely due to human activities on land and at sea. Climate change occurred later and is likely to impact mud and sand transport in the future. The degradation is still increasing because the management decisions suffer from the shifting baseline syndrome. For sustainable management, a holistic, ecohydrology-based approach is needed. It must involve all stakeholders and integrates hydrotechnical, biophysical and social approaches over the whole watershed including Magnetic Island, and all coastal waters. Several such solutions are proposed. These solutions may be applicable to all Queensland ports facing the Great Barrier Reef, as they all suffer from similar issues to various degrees.

Oceanographic Processes of Coral Reefs, D. Suzuki The Place of Science and Technology in the Wise Management of the Great Barrier Reef, J. Baker Physics-Biology Links in the Great Barrier Reef, E. Wolanski Landcover and Water Quality in River Catchments of the Great Barrier Reef Marine Park, A.K.L. Johnson et al. Runoff of Terrestrial Sediment and Nutrients into the Great Barrier Reef World Heritage Area, M. Furnas and A. Mitchell Water Circulation in Mangroves, and Its Implications for Biodiversity, E. Wolanski et al. Muddy Coastal Waters and Depleted Mangrove Coastlines - Depleted Seagrass and Coral Reefs, N.C. Duke and E. Wolanski The Effects of Siltation on Tropical Coastal Ecosystems, M. Fortes Modeling and Visualizing Interactions Between Natural Disturbances and Eutrophication as Causes of Coral Reef Degradation, L.J. McCook et al. Biodiversity on the Great Barrier Reef: Large-Scale Patterns and Turbidity-Related Local Loss of Soft Coral Taxa, K. Fabricius and G. De'ath River Plume Dynamics in the Central Great Barrier Reef, B. King et al. Connectivity in the Great Barrier Reef World Heritage Area - An Overview of Pathways and Processes, M. Cappo and R. Kelley A Model of the Ecosystem, and Associated Penaeid Prawn Community in the Far Northern Great Barrier Reef, N.A. Gribble The Effects of Water Flow Around Coral Reefs on the Distribution of Pre-Settlement Fish (Great Barrier Reef, Australia) J.H. Carleton et al. Topographic Steering by Coral Reef Assemblages, S. Spagnol et al. Environmental Factors Influencing the Activity of Black Marlin, P. Speare and C.R. Steinberg Ocean Nutrients to Sediment Banks via Tidal Jets and Halimeda Meadows, E.A. Drew Climate Variability and Change on the Great Barrier Reef, J.M. Lough The Sea Surface Temperature Story on the Great Barrier Reef During the Coral Bleaching Event of 1998, W. Skirving and J. Guinotte The Challenges of Coral Reef Management in Indonesia, I.M. Dutton et al. Will the Great Barrier Reef Survive Human Impact? F. H. Talbot

This paper evaluates the conditions experienced by water-born passive larvae of broadcast spawning coral and crown-of-thorn starfish and how they self-recruit to their natal reefs in the Great Barrier Reef. The hypothesis that passive larvae are trapped for extended periods around specific areas of their natal reef (100s of metres) was found to be generally invalid. However, at some sites long-term trapping may occur when flow separation at headlands and in reef passages creates recirculating flows in embayments and behind concave-shaped reefs. Linear reefs do not trap passive larvae. This was demonstrated using satellite images and oceanographic modeling. The degree of self-recruitment at locations depended on the details of the incident flow speed, the shape of the headlands and the reef passages, the orientation of the reef compared to that of the tidal currents, the aspect ratio of the embayment, the curvature of the reef, and the time that the developing mushroom tidal jets takes to pass in front of the embayment. Self-recruitment of passive larvae depends on the spatial scale; at scales of 100s of metres, it is a rare process in the Great Barrier Reef. An exception was in a high-density reef matrix where the sticky water effect prevailed and self-recruitment was higher. Further, at scales of whole reefs (kilometres) and clusters of reefs (kms to 10s of kilometres) the likelihood of self-recruitment was higher. The probability of self-recruitment for reef fish larvae swimming directionally to their natal reefs following auditory and chemical cues is predicted to be much higher.

The Great Barrier Reef (GBR; Figure 1), together with its 424,000 km2 catchment comprising 35 rivers, is enormous. It is nearly 2,000 km long, it has about 2,500 reefs of various sizes and shapes, and these reefs are scattered in diverse ways in different regions of the continental shelf. The shelf width and depth vary with latitude between 30 and 200 km, and its mean depth also varies with latitude between 30 and 100 m. It borders the Coral Sea with depths of 2,000–4,000 m.

The ocean is a three-dimensional environment that has a great influence on the movement of particulate matter, sediments, plankton, and nekton. The complexity of currents increases greatly in mosaics of coral reefs, and here, we focus on the interactions among physical oceanography, biology, and abiotic particles that include pollutants.

In marine, coastal and estuarine environments, it is not possible to understand the ecological processes unless there is a very good understanding of the physical forcing factors. In turn, once the physics of an area creates the conditions for colonisation by the biota, then, very often, the biota modifies the physical and biogeochemical processes. This review details the physical processes involved both in the substratum and the water column, especially in muddy sedimentary systems typical of estuaries and coastal areas. Using recent studies to show that the physical and biological structure and processes work in tandem to create the water column and sedimentary features, the analysis shows that the physics creates the conditions both for chemical mediation and for biological colonisation. The responses on and by the biota include both the micro- and macroorganisms that influence flocculation, floc creation and disintegration, especially through the production of extracellular mucous substances, bioerosion and biostabilisation. Colonisation is firstly by microorganisms and then by macroorganisms. These organisms then create feedback loops where they modify the structure of both the flocs and the bed sediment. It is emphasised that these aspects need to be incorporated into the engineering models of fine sediment dynamics of estuarine and coastal waters, in order to increase their reliability.

This chapter aims to develop an ecohydrological modelling approach to propose an environmental engineering solution based on historical nature-based information to alleviate the severe water degradation problem within Luanda Bay, Angola. This solution would improve local communities' ecosystem health and quality of life. The model suggests a simple and practical solution to solving the pollution problem by opening a cut from the bay's shallows to the sea. This will essentially reproduce an old bay opening to the sea, which was filled early in the last century. The residence time of water in the shallows of Luanda Bay would be reduced to about one week by excavating the channel over the land is straightforward. This should return the system to a more natural state and improve the water quality for recreational activities, increase the quality of marine food resources, reduce toxic algae blooms, and improve the quality of life of people in the area. Nevertheless, preventing pollutants from reaching Luanda Bay is the only long-term solution to restore a healthy environment in Luanda Bay

Here, we emphasise a fundamental difference between the shelf waters of the Great Barrier Reef (GBR) and other parts of the world. The water circulation over the GBR continental shelf, like that of continental shelves worldwide, is strongly influenced by the circulation in the adjoining sea. This circulation is dominated by the South Equatorial Current that is highly mesoscale turbulent and takes the form of jets and eddies. As these jets approach the continental shelf, they bifurcate to the north and south. Commonly, shelf waters have a gentle slope, with few shoals, islands, and reefs until the shelf break. In contrast, the GBR has approximately 2,500 reefs, resulting in a flow field largely uncorrelated with the mesoscale turbulence in the adjoining Coral Sea. The currents among reefs are generally dominated by strong tidal currents, topographic eddies, jets, topographically driven upwelling and downwelling, shear zones, stagnation zones, and topographically steered flows. The reefs generate a 'bioengineered' physical oceanography dominated by a number of processes including (1) Bernoulli tidal upwelling in reef passages, (2) inflow of oceanic water from wave breaking at the reef crests, (3) swift tidal flow through reef passages and the channelisation of the tidal flow on the shelf, (4) the wind deflecting intruding oceanic water back out to sea, (5) deflection of the mean currents around a reef matrix through the 'sticky water' effect, (6) convergence of opposing tidal waves in the southern GBR, and (7) reduction by the reefs of the inflow into the GBR from oceanic water.

Remote, data-limited marine environments are poorly understood, making conservation and resource manage-ment major challenges in the rapidly changing environment. High field data collection costs results in sparse data, which limits the traditional scientific approach to understand the functioning of these remote ecosystems. The Gulf of Carpentaria is a vast, remote and data-limited region in northern Australia that is vulnerable to rapid changes due to climate change and externally derived marine debris, but extremely difficult and costly to access. This study aimed to test a method of improving certainty in ecological and physical processes in the Gulf of Carpentaria by maximising the use of alternative biophysical data from local Indigenous-owned and managed land and sea country, to elucidate the ecosystem functioning. We investigated the role of currents and wind in previously published Green turtle (Chelonia mydas) post-nesting satellite tracking migration data, and found they had no influence on the turtles' migration path. We also found that turtles did not use compass bearing alone to make their migration, rather they seemingly used coastal cues to 'leap-frog' along the coastline until they reached their foraging grounds. Next, we identified the spatio-temporal distribution of floating marine plastics using Indigenous-lead citizen science coastal marine debris surveys, and found that previous studies have underestimated marine debris presence in the region. Finally, biophysical modelling suggests that large migra-tions (>200 km in 28-35 days) of tagged male Giant mud crabs (Scylla serrata) against prevailing winds, currents and tides were possible by using selective tidal stream transport and directional swimming. These case-studies demonstrate the effectiveness of explorative biophysical modelling supported by alternative field data, and improve certainty in ecological processes with significance in culture, conservation and commercial values in the region.

Despite the lack of obvious physical barriers and their ability to travel significant distances, many marine mammals exhibit substantial population structuring over relatively short geographical distances. The dugong (Dugong dugon), the only extant representative of family Dugongidae, is listed as Vulnerable to Extinction globally. We investigated the genetic population structure of dugongs in the shallow coastal waters along >2,000 km of the eastern Queensland coast, including the Great Barrier Reef region. Microsatellite genotypes for 22 loci in 293 dugongs, SNP genotypes based on 10,690 loci in 43 dugongs, and 410 bp mitochondrial control-region sequences from 639 dugongs were analyzed. Clustering analysis techniques consistently identified an abrupt genetic break in the Whitsunday Islands region (20.3 degrees S), which interrupts an overall pattern of isolation-by-distance. Geographic distance was relatively more important than sea-surface temperature and seagrass distribution in explaining pairwise microsatellite genetic distances. The cause of reduced dispersal across this region is unknown but might relate to an unusual tidal and current mix, termed the "sticky-water" effect, and/or a break in the geographical distribution of off-shore seagrass meadows. The genetic structure suggests distinct breeding units north and south of the Whitsunday Islands region for consideration in further developing management plans for Queensland dugongs.

Chapter 3 Reproduction, Ontogeny and Recruitment Edward D. Houde, Edward D. HoudeSearch for more papers by this authorKenneth W. Able, Kenneth W. AbleSearch for more papers by this authorNadine A. Strydom, Nadine A. StrydomSearch for more papers by this authorEric Wolanski, Eric WolanskiSearch for more papers by this authorTimo Arula, Timo ArulaSearch for more papers by this author Edward D. Houde, Edward D. HoudeSearch for more papers by this authorKenneth W. Able, Kenneth W. AbleSearch for more papers by this authorNadine A. Strydom, Nadine A. StrydomSearch for more papers by this authorEric Wolanski, Eric WolanskiSearch for more papers by this authorTimo Arula, Timo ArulaSearch for more papers by this author Book Editor(s):Alan K. Whitfield, Alan K. Whitfield South African Institute for Aquatic Biodiversity, Grahamstown, South AfricaSearch for more papers by this authorKenneth W. Able, Kenneth W. Able Rutgers University, Tuckerton, USASearch for more papers by this authorStephen J.M. Blaber, Stephen J.M. Blaber CSIRO Oceans & Atmosphere, Brisbane, AustraliaSearch for more papers by this authorMichael Elliott, Michael Elliott IECS Ltd, Leven, UK University of Hull, Hull, UKSearch for more papers by this author First published: 18 February 2022 https://doi.org/10.1002/9781119705345.ch3Citations: 9 AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Summary This chapter reviews and synthesises knowledge on reproduction and recruitment in estuary-dependent and estuary-associated fishes. Resident and migrating species (anadromous, catadromous and amphidromous) capitalise on estuarine productivity to ensure successful reproduction. The variable estuarine environments are challenging, but many species are adapted to reproduce in and recruit to these rich and productive ecosystems. Modes of reproduction, including utilisation of nursery habitat by early-life stages and behavioural adaptations, are described, as are contributions of adults to recruitment. Scales and patterns of environmental, hydrodynamic and biological processes that control ingress or retention of early-life stages in estuaries are reviewed. Recruitment processes in estuary-associated species are highly dynamic, depend on fish behaviour, are variably dependent on adult abundance and are difficult to predict. Case studies and global examples are presented to highlight the diversity of strategies and factors that ensure reproductive success. Citing Literature Fish and Fisheries in Estuaries: A Global Perspective RelatedInformation

This study documents the impact of climate change and human activities on the Burdekin River delta and coast. The Burdekin River is located in the dry tropics with a seasonally and interannually highly variable discharge, controlled by occasional cyclones and the ENSO-dependent monsoon. Even though the peak discharge from cyclonic rainfall is decreased by a dam, large floods still occur during long-duration monsoon. While the dam traps much of the coarse sediment runoff, large amounts still reach the Delta originating from catchments downstream of the dam. The riverbed in the Delta has measurably risen in recent decades. In turn, this increases the flood levels and the threat of channel avulsion. Sand trapping by the dam and in the Delta is also starving the coast of sand, and this generates rapid coastal erosion along the 11 km long Cape Bowling Green peninsula. Climate change is enhancing this coastal erosion as in the last few decades the mean sea level and the frequency of strong winds have increased significantly. The peninsula may breach soon. As the peninsula protects Ramsar-listed wetlands of international significance, its breaching is predicted to impact the fisheries that depend on the Cape (the black marlin billfish) and on the wetlands (mud crabs, barramundi and mangrove jacks), as well as shorebirds and waterbirds. These findings demonstrate the connectivity of water and sediment throughout the river basin and the coast, and the need for management at the basin scale using ecohydrology principles.

For many years, local communities have expressed concerns that turbid plume waters from the Fly River in Papua New Guinea may potentially deliver mine-derived contaminants to the Torres Strait, an ecologically and culturally unique area north of the Australian mainland. Information on suspended sediment transport and turbidity patterns are needed in this data-limited region to identify and manage downstream ecosystems that may be at risk of exposure from the Fly River runoff. This study used MODIS satellite time series and a colour-classification approach to map optical water types around the data-poor Gulf of Papua and Torres Strait region. The satellite data were supported by field data, including salinity and suspended sediment measurements, and used together in qualitative water quality assessments to evaluate the habitats that are likely exposed to Fly River discharge and/or derived sediments. It showed that the Fly River influence in the Torres Strait region is largely limited to the north-east corner of the Torres Strait. The drivers of turbidity vary between locations, and it is impossible to fully separate direct riverine plume influence from wave and tidally driven sediment resuspension in the satellite maps. However, results indicate that coastal habitats located as far east as Bramble Cay and west to Boigu Island are located in an area that is most likely exposed to the Fly River discharge within the region, directly or through sediment resuspension. The area that is the most likely exposed is a relatively small proportion of the Torres Strait region, but encompasses habitats of high ecological importance, including coral reefs and seagrass meadows. Satellite data showed that the period of highest risk of exposure was during the south-east trade wind season and complemented recent model simulations in the region over larger spatial and temporal frames. This study did not evaluate transboundary pollution or the ecological impact on local marine resources, but other recent studies suggest it is likely to be limited. However, this study did provide long-term, extensive but qualitative, baseline information needed to inform future ecological risk mapping and to support decision making about management priorities in the region. This is important for ensuring the protection of the Torres Strait ecosystems, given their importance to Torres Strait communities and turtle and dugong populations, and the Torres Strait’s connectivity with the Great Barrier Reef Marine Park.

A 30-year time series of the recruitment of rabbit fish, a herbivorous coral reef fish, on the island of Guam in the tropical western Pacific, showed variability that ENSO alone does not explain. To help explain this variability, a high-resolution biophysical model that includes directional swimming reveals how mesoscale turbulence and ENSO-driven changes in the ocean circulation control the self-recruitment of rabbit fish. ENSO drives island wakes that enhance the capacity to retain locally spawned larvae, and mesoscale turbulence generates much variability and promotes seaward dispersion at time scales larger than the Pelagic Larval Duration. The same processes are predicted to occur for the self-recruitment of grouper fish, a carnivorous coral reef fish, in Palau, Micronesia. The models suggests that 99% of these fish larvae are exported seaward from Guam and Palau. Those larvae are the ones that could provide connectivity between reefs and islands in Micronesia. This connectivity for the grouper fish was predicted using an altimetry-driven advection-diffusion oceanography model for 40 mass spawning events spread over 10 years. The mesoscale turbulence, and not the mean oceanographic currents, is the dominant process controlling the connectivity, which is thus chaotic. This finding applies also in the Galapagos archipelago and the Coral Sea fringing the Great Barrier Reef.

Cubozoan jellyfish are classified as plankton despite the strong swimming and orientation abilities of cubomedusae. How these capabilities could affect cubozoan population structures is poorly understood. Medusae of the cubozoan Copula sivickisi can uniquely attach to surfaces with the sticky pads on their bells. Biophysical modelling was used to investigate the spatial scales of connectivity in a C. sivickisi population. When the medusae were active at night they could maintain their observed distribution on fringing reef if they attached to the reef when the current speed exceeded a moderate threshold. This behaviour facilitated the isolation of a C. sivickisi population on reefs fringing Magnetic Island, Queensland, Australia. Within this distribution, there was considerable within bay retention and medusae rarely travelled > 3 km. The few (< 0.1%) medusae lost from the island habitat were largely advected into open water and away from the mainland coast which lies 8 km from the island. Given that successful emigration is unlikely, the island population probably represents a stock that is ecologically distinct from any mainland populations. The cosmopolitan distribution of C. sivickisi could contain incipient or cryptic species given the small scales of connectivity demonstrated here.

Availability of water for wildlife in some of the National Parks in Tanzania has been hampered by several factors including the effect of climate change and anthropogenic factors due to the fact that most of the water catchments are outside the national parks. In order to ensure the survival of the National Parks, TANAPA, which is a Parastatal Organization mandated to manage the National Parks, has taken proactive initiatives and actions to tackle the water crisis in its National Parks, principally the Serengeti, Tarangire, Ruaha, Katavi, Rubondo, Saadani, Arusha and Kilimanjaro National Parks. These initiatives and actions have followed the ecohydrology guidelines for water management and they varied from Park to Park according to the local conditions. There are limits to what TANAPA can achieve by itself to save its National Parks from the water crisis, because TANAPA has no control on activities outside the Parks. For those water issues TANAPA has communicated its findings and recommendations to the government and stakeholders, and the resolution, or otherwise, of these issues requires state governance as well as in some cases cooperation between the East African countries.