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Anthropogenic changes to river flows can alter hydrological connectivity and cues necessary for the movement of fish to complete their life cycles. Quantifying flow-related movement ecology of fish and understanding how this varies between species and river systems is important for effective environmental flow management. This study aimed to determine hydroecological factors that influence fish movements in an unregulated, perennial river and to compare these findings to fish from regulated river systems. Broad-scale movements of the endangered Maccullochella ikei and Tandanus tandanus were recorded over 3 years in the unregulated, perennial Nymboida River, Australia. The limited movements both species exhibited were infrequent and over short distances. Although M. ikei movements appeared mostly unrelated to environmental changes, T. tandanus moved on flow pulse peaks and were more likely to move during the breeding season. These findings contrast with previous studies of the same or similar species in differing flow regimes, suggesting that fish in perennial, highly connected rivers may not need to move as frequently as those in more regulated or intermittent systems. Should these disparate behaviours be present in other species occurring among contrasting flow regimes, it will be challenging to define generalisable environmental flow rules to inform river management.

Both brown (detrital-based) and green (algal-based) food pathways support freshwater food webs, although the importance of either source may vary within species, regions and different phases of the flow regime. The bony bream (Nematalosa erebi Clupeidae: Dorosomatinae) is one of Australia's most widely distributed freshwater fish species and is a key component of freshwater food webs, especially in northern Australia. We sought to better define the feeding habits of this species, previously classified as a detritivore, algivore or zooplanktivore (or combinations thereof), by undertaking meta-analyses of published accounts based on stomach content analysis and 13C and 15N stable isotope analysis. Stomach content analysis clearly indicated that detritus was the dominant food item, although benthic algae could be an important dietary component in some habitats (inland river flood plains) and during the wet season. Zooplankton were important for small fish (i.e. juveniles 13C enriched, indicating the latter source was not the dominant contributor to the biomass of this species. However, using site-specific data and a regression approach, a significant relationship was revealed between algal carbon and that of large fish, suggesting that carbon derived from benthic algae contributed ~20% of the carbon of adult bony bream. Zooplankton contributed a similar amount. Zooplankton provided the majority of carbon for small fish. We contend that detritus derived from terrestrial vegetation is the likely remaining carbon source for large bony bream, and this interpretation was supported by the outcomes of multiple regression analyses. Although previous studies of aquatic food webs in northern Australia have emphasised the importance of high-quality algal basal resources, this study indicates that terrestrial sources may be important for some species and demonstrates the need to better consider the circumstances that cause biota to switch between different food sources.

Both brown (detrital-based) and green (algal-based) food pathways support freshwater food webs, although the importance of either source may vary within species, regions and different phases of the flow regime. The bony bream (Nematalosa erebi Clupeidae: Dorosomatinae) is one of Australia’s most widely distributed freshwater fish species and is a key component of freshwater food webs, especially in northern Australia. We sought to better define the feeding habits of this species, previously classified as a detritivore, algivore or zooplanktivore (or combinations thereof), by undertaking meta-analyses of published accounts based on stomach content analysis and 13C and 15N stable isotope analysis. Stomach content analysis clearly indicated that detritus was the dominant food item, although benthic algae could be an important dietary component in some habitats (inland river flood plains) and during the wet season. Zooplankton were important for small fish (i.e. juveniles

Globally, freshwater fishes are declining at an alarming rate. Despite much evidence of catastrophic declines, few Australian species are listed as threatened under national legislation. We aim to help redress this by identifying the Australian freshwater fishes that are in the most immediate risk of extinction. For 22 freshwater fishes (identified as highly threatened by experts), we used structured expert elicitation to estimate the probability of extinction in the next ~20 years, and to identify key threats and priority management needs. All but one of the 22 species are small (50% probability of extinction in the next ~20 years. Collectively, the biggest factor contributing to the likelihood of extinction of the freshwater fishes considered is that they occur in small (distributions ≤44km2), geographically isolated populations, and are threatened by a mix of processes (particularly alien fishes and climate change). Nineteen of these species are unlisted on national legislation, so legislative drivers for recovery actions are largely absent. Research has provided strong direction on how to manage ~35% of known threats to the species considered, and, of these, ~36% of threats have some management underway (although virtually none are at the stage where intervention is no longer required). Increased resourcing, management intervention and social attitudinal change is urgently needed to avert the impending extinction of Australia’s most imperilled freshwater fishes.

Catadromous fish species often use elevated flows to migrate from freshwater to downstream spawning grounds. However, in regulated river systems, artificial barriers and flow alteration can disrupt movement cues, affecting fish migration. Using a combination of acoustic telemetry, passive integrated transponder (PIT) tags and gonad maturity data, we assessed the migratory timing and flow requirements for downstream spawning migrations and upstream dispersal in two co-occurring mullet species in the Logan River, eastern Australia. Over 4 years, 141 adult sea mullet (Mugil cephalus) and 28 adult pinkeye mullet (Trachystoma petardi) were implanted with acoustic transmitters and broad-scale movements tracked using an array of 49 acoustic receivers. Juvenile upstream dispersal was monitored using implanted PIT tags and readers deployed in weir fishways. Sea mullet and pinkeye mullet undertook large-scale downstream migrations from February to March. Movements past weirs only occurred once sufficient flow had occurred and, in the case of pinkeye mullet, when gonads were mature. In contrast, juvenile dispersal into upstream habitats occurred primarily between November and April on low flows. This study advances our understanding of bidirectional movement ecology and flow requirements of two co-occurring mullet species to inform environmental flow management (e.g. to facilitate fish passage) in a regulated river system.

The aim of the present study was to determine whether boat-based deployment of remote underwater video cameras is effective for surveying fish assemblages in the deepest reaches of two large tropical rivers in north-eastern Australia. In addition, we compared fish assemblages recorded on baited versus unbaited cameras, and evaluated the sampling effort (duration of recording) required to estimate fish assemblages using remote underwater videos. We found that fish assemblages differed according to the depth, with statistically significant differences largely attributable to the prevalence of small-bodied species (10cm TL), such as Lutjanus argentimaculatus, Mesopristes argenteus and Caranx sexfasciatus, in deep water (>5.0m). Estimates of fish assemblage attributes generally stabilised after 60min recording duration, suggesting that interrogation of video footage beyond this duration may not be cost-effective. We conclude that depth is an important consideration when surveying large and deep river fish assemblages and that where water clarity is favourable, underwater video provides one of the means by which an assemblage can be investigated across the entire depth profile.

Catadromous fish species require adequate flows to migrate between fresh and saltwater habitats to reproduce. However, artificial barriers and flow alteration affect fish populations by reducing habitat connectivity and disrupting movement cues. In regulated rivers, it is critical that migratory flow requirements are quantified to optimise water allocation for multiple users. In the present study, we assessed the migratory timing, flow and estuarine aggregation requirements for Australian bass (Percalates novemaculeata). Over 2 years, 66 bass were tracked using an acoustic receiver array in the Logan River (Qld, Australia). Bass performed large-scale downstream movements in response to elevated winter flows (40 and 108m3 s–1), which facilitated migration to the lower estuary, where salinity conditions were appropriate for spawning. Bass migrations occurred only when gonads were mature, despite large flows providing opportunities for movement outside this period. Experimental flow releases from an impoundment (2.1m3 s–1) during winter did not elicit a migratory response. Connectivity between upstream and estuarine habitats was reduced by the presence of instream weirs, with downstream movement across weirs occurring only when sufficient flow magnitude was achieved (>76.1m3 s–1). These findings are relevant for water resource managers formulating environmental flow rules for catadromous fish species in systems with multiple instream artificial barriers.

The aim of the present study was to determine whether boat-based deployment of remote underwater video cameras is effective for surveying fish assemblages in the deepest reaches of two large tropical rivers in north-eastern Australia. In addition, we compared fish assemblages recorded on baited versus unbaited cameras, and evaluated the sampling effort (duration of recording) required to estimate fish assemblages using remote underwater videos. We found that fish assemblages differed according to the depth, with statistically significant differences largely attributable to the prevalence of small-bodied species (Ambassis sp., Melanotaenia sp. and Pseudomugil signifer recorded in shallow (0.4–2.0m) and intermediate (2.1–4.9m) depths, and larger-bodied fish species (>10cm TL), such as Lutjanus argentimaculatus, Mesopristes argenteus and Caranx sexfasciatus, in deep water (>5.0m). Estimates of fish assemblage attributes generally stabilised after 60min recording duration, suggesting that interrogation of video footage beyond this duration may not be cost-effective. We conclude that depth is an important consideration when surveying large and deep river fish assemblages and that where water clarity is favourable, underwater video provides one of the means by which an assemblage can be investigated across the entire depth profile.

Key issues with defining reference condition for stream bioassessment are (1) equivocal definitions of ‘minimally disturbed’ pressure criteria and wide-ranging approaches to site selection, (2) highly modified regions where near-pristine areas do not exist, leading to management decisions based on inconsistent and unquantified benchmarks and (3) costly field campaigns associated with ‘extensive spatial survey’ approaches. We used generalised dissimilarity modelling (GDM) to classify stream segments into ecotypes, and transparently and efficiently define candidate reference conditions for the Ecosystem Health Monitoring Program (EHMP) assessment area in south-eastern Queensland, a highly modified region with a complex biogeographic history. We modelled fish presence–absence data from 396 sites with GIS-based natural and anthropogenic predictors. Stream segments were classified into ecotypes using the GDM-transformed natural variables so that (1) reference-site selection adequately covered the β-diversity of the study area and (2) we could evaluate the validity of incorporating sites from neighbouring catchments outside of the EHMP assessment area. Relationships between selected anthropogenic variables (the river disturbance index and %stream connectivity) and fish assemblages were used to define pressure criteria and map candidate reference conditions. We conclude by describing a new framework that can be used to select indicator-specific reference sites by GDM and a stratified, probabilistic sampling design.

Estuaries are recognised globally as areas of high production, diversity and high economic value. Exploitation of the economic potential of estuaries and attendant infrastructural development plus expansion of human populations has resulted in degradation of estuaries worldwide. Many estuaries of northern Australia, in contrast, remain in good ecological condition. The estuarine fish fauna of the South Alligator River, Kakadu region of northern Australia was investigated to determine seasonal and spatial variation in composition. Beam trawls were used at 94 locations over the wet and dry seasons of 2012. In total, 81 taxa were collected, 26 of which had not previously been recorded in the river. Sciaenidae and Engraulidae dominated species richness and abundance. Samples were heterogeneous in terms of composition and abundance in a manner unrelated to any measured aspect of the habitat over which trawls occurred. Species richness was higher in the lower estuary than the upper estuary and more species were detected during the wet season. Turnover in assemblage structure between sampling occasions was associated with seasonal variation in discharge concordant with changes in salinity and potentially productivity. Compositional variation was largely ascribed to differential spawning phenology of adults and tolerance to fluctuating salinity. The Kakadu region supports a rich fish fauna moderately distinct from that observed elsewhere in the Northern Territory. Pronounced temporal turnover in assemblage structure and spatial variation at a variety of scales (i.e. within samples, and within and between rivers) collectively pose a challenge to management in light of ongoing and proposed development of the water resources of northern Australia, including its estuaries.

Freshwater Fishes of North-Eastern Australia provides details of the ecology, systematics, biogeography and management of 79 species of native fish present in the region. It includes detailed information on their identification, evolutionary history, breeding biology, feeding ecology, movement patterns, macro-, meso- and micro-habitat use, water quality tolerances, conservation status and current threats, as well as environmental flow and management needs. Based on the results of extensive field surveys and a comprehensive review of existing literature, it is designed to assist environmental practitioners and managers to make informed decisions about future management strategies. It will also encourage a greater research effort into the region’s aquatic fauna by providing a comprehensive resource that enables other researchers to adopt a more quantitative and strategic framework for their research. Joint winner of the 2005 Whitley Medal.

Dense tropical rainforest, waterfalls and shallow riffle-run-pool sequences pose challenges for researcher access to remote reaches of streams for surveying aquatic fauna, particularly when using capture-based collecting techniques (e.g. trapping, backpack and boat electrofishing). We compared the detection of aquatic species (vertebrates and invertebrates >1cm in body length) within pool habitats of a rainforest stream obtained by two visual techniques during both the wet and dry season: active visual survey by snorkelling and baited remote underwater video stations (BRUVSs). Snorkelling detected more species than a single BRUVS at each site, both within and among seasons. Snorkelling was most effective for recording the presence and abundance of diurnally active small-bodied species (adult size

The 2013 Acreage Release Areas W13-19 and W13-20 in the offshore northern Perth Basin, Western Australia, cover more than 19,000 km2 in parts of the Houtman, Abrolhos, Zeewyck and Gascoyne sub-basins. The Release Areas are located adjacent to WA-481-P, the only active offshore exploration permit in the Perth Basin, granted to joint venture partners Murphy Australia Oil Pty Ltd, Kufpec Australia Pty Ltd and Samsung Oil and Gas Australia Pty Ltd in August 2012. Geoscience Australia recently undertook a regional prospectivity study in the area as part of the Australian Government’s Offshore Energy Security Program, which provides fresh insights into basin evolution and hydrocarbon prospectivity. A sequence stratigraphic framework, based on new biostratigraphic sampling and interpretation, and an updated tectonostratigraphic model, using multiple 1D burial history models for Permian to Cenozoic sequences, have been developed. New geochemical studies of key offshore wells demonstrate that the oil-prone source interval of the Lopingian–Lower Triassic Hovea Member extends regionally offshore into the Abrolhos Sub-basin and potentially as far as the Houtman Sub-basin. This is supported by fluid inclusion data that provide evidence for palaeo-oil columns within Permian reservoirs in wells from the Abrolhos Sub-basin. Oil trapped in fluid inclusions in Houtman-1 can be linked to Jurassic source rocks, suggesting that multiple petroleum systems are effective in the Release Areas. The presence of active petroleum systems is also supported by the results of a recent marine survey. Potential seepage sites on the seafloor over reactivated faults correlate with hydroacoustic flares, pockmarks and dark colored viscous fluids that were observed over the areas. This may indicate an active modern-day petroleum system in the Houtman Sub-basin. Finally, a trap integrity analysis was undertaken to mitigate exploration risks associated with trap failure during Early Cretaceous breakup and provides a predictive approach to prospect assessment. These results provide strong support for the presence of active petroleum systems in the offshore northern Perth Basin and upgrade the prospectivity of the Release Areas.

The discovery of commercial oil in the Cliff Head-1 well in 2001 set an important milestone in the exploration history of the offshore northern Perth Basin. The region had been less explored before then, partly due to the perception that the main source of onshore petroleum accumulations, the Late Permian-Early Triassic Hovea Member, had only marginal potential offshore. The typing of the Cliff Head oil to the Hovea Member provided evidence that the key onshore petroleum system extends offshore and has revitalised exploration with 13 new field wildcat wells drilled since 2002. A reassessment of the hydrocarbon generative potential in the offshore northern Perth Basin confirms the widespread occurrence of good to excellent oil-prone Hovea Member source rocks in the Beagle Ridge and Abrolhos Sub-basin. The Early Permian Irwin River Sequence and several Jurassic Sequences are also recognised as prime potential source rocks offshore, mostly for their gas-generative potential. The unique hydrocarbon assemblages exhibited by the Hovea Member extracts are shared by the oils recovered from Permian reservoirs in the offshore Cliff Head-3 and Dunsborough-1 wells, indicating the Hovea Member as the primary source charging these accumulations. Geochemical correlation of oil stains from Hadda-1 and as far north as Livet-1 provides evidence for a working Early Triassic petroleum system across much of the Abrolhos Sub-basin. In this area, the Hovea Member was shown to be both of limited quality and only marginally mature for oil generation, which suggests the occurrence of effective source kitchens in the adjacent Houtman Sub-basin.

The presence of hydrocarbon accumulations and several palaeo-oil columns in Permian reservoirs across the offshore northern Perth Basin attests to a widespread charge system and suggests that trap integrity is a critical exploration risk. The local structural evolution between the Beagle Ridge and the Wittecarra Terrace and the impact of renewed mid-Jurassic extension on a series of prospects (Cliff Head, Dunsborough, Lilac and Morangie) is assessed to define a regional trap integrity framework. The focus is on the potential development of pathways through the Early Triassic Kockatea Shale regional top seal caused by reactivation of trap bounding faults and/or interaction with newly formed overlying structures. A series of 3D geo-mechanical models are constructed to simulate the Mid-Jurassic deformation and to evaluate the first-order factors controlling the partitioning of reactivation stresses/strains and the development of seal bypass. In parallel, the local fault seal potential is assessed by focusing on the likelihood of the fault surfaces to reactivate and conduct fluid within the Jurassic stress regimes. The stress data are also used to compute the risk of reactivation in terms of the increase in pore fluid pressure required to bring a fault segment to a state of instability. The overall risk of top seal bypass is primarily driven by the reservoir-bounding faults orientation and dip. The distribution of jogs, the interactions between fault tips, the fault density, the location of regional major fault, the fault propagation mechanisms and top seal brittleness also control locally the integrity of the top seal.

Freshwater environments and their fishes are particularly vulnerable to climate change because the persistence and quality of aquatic habitat depend heavily on climatic and hydrologic regimes. In Australia, projections indicate that the rate and magnitude of climate change will vary across the continent. We review the likely effects of these changes on Australian freshwater fishes across geographic regions encompassing a diversity of habitats and climatic variability. Commonalities in the predicted implications of climate change on fish included habitat loss and fragmentation, surpassing of physiological tolerances and spread of alien species. Existing anthropogenic stressors in more developed regions are likely to compound these impacts because of the already reduced resilience of fish assemblages. Many Australian freshwater fish species are adapted to variable or unpredictable flow conditions and, in some cases, this evolutionary history may confer resistance or resilience to the impacts of climate change. However, the rate and magnitude of projected change will outpace the adaptive capacities of many species. Climate change therefore seriously threatens the persistence of many of Australia’s freshwater fish species, especially of those with limited ranges or specific habitat requirements, or of those that are already occurring close to physiological tolerance limits. Human responses to climate change should be proactive and focus on maintaining population resilience through the protection of habitat, mitigation of current anthropogenic stressors, adequate planning and provisioning of environmental flows and the consideration of more interventionist options such as managed translocations.

A widespread charge system for oil accumulation in the offshore northern Perth Basin, Western Australia, is revealed by specialised fluid inclusion technologies. Palaeo-oil columns are detected in about three of four exploration wells, including those at the Cliff Head, Dunsborough, Frankland and Perseverance fields, and in dry wells at Flying Foam–1, Hadda–1, Houtman–1, Leander Reef–1, Lilac–1, Livet–1, Mentelle–1 and Morangie–1. A high incidence of palaeo-oil charge into Permian reservoirs below the Kockatea Shale confirms that the conventional oil shows are, in part, residues of palaeo-oil. Oil migration is suggested at Vindara–1 and Leander Reef–1 and is below detection limits in Batavia–1, Charon–1, Fiddich–1 Geelvink–1A, Gun Island–1 and South Turtle Dove–1B, Twin Lions–1 and Wittecarra–1. New geochemical data from fluid inclusion oil at Hadda–1 shows evidence for a contribution from the Hovea Member of the Kockatea Shale, including: high wax content; low pristane/phytane ratio; high abundance of extended tricyclic terpanes; and, the highly diagnostic C33 n-alkylcyclohexane biomarker. This key component of the petroleum system acted as both source and seal, and extends further offshore than previously realised. Possible co-sourcing from terrestrial organic matter is indicated by high abundances of C29 steranes and diasteranes, C19 tricyclic, and C24 tetracyclic terpanes, which may be sourced from Permian rocks. The high incidence of palaeo-oil and residual columns suggests that trap integrity is likely to be an important preservation risk, with elements of gas displacement. Screening of prospects for structural and hydrocarbon charge characteristics, which are favourable for retention of oil, is key in future exploration of the offshore northern Perth Basin.

Numerous Miocene reefs and related carbonate build-ups have been identified in the Rowley Shoals region of the central North West Shelf, offshore Western Australia. The reefs form part of an extensive Miocene reef tract over 1,600 km long, which extended northward into the Browse and Bonaparte basins and southward to North West Cape in the Carnarvon Basin—comparable in length to the modern Great Barrier Reef. Growth of the vast majority of these Miocene reefs failed to keep pace with relative sea-level changes in the latest Miocene, whereas reef growth continued on the central North West Shelf to form the three present-day atolls of the Rowley Shoals: Mermaid, Clerke and Imperieuse reefs. In the Rowley Shoals region, scattered small build-ups and local reef complexes were first established in the Early Miocene, but these build-ups were subsequently terminated at a major Mid Miocene sequence boundary. Widespread buildups and atoll reefs were re-established in the Middle Miocene, and the internal stacking geometries of the reefs appear to relate to distinct growth phases that are correlated with eustatic sea-level fluctuations. These geometries include: a basal aggradational buildup of early Middle Miocene age; a strongly progradational growth phase in the late Middle to early Late Miocene that constructed large reef atolls with infilling lagoon deposits; and a back-stepped aggradational growth phase that formed smaller reef caps in the early–latest Late Miocene. Growth of the majority of the reefs ceased at a major sea-level fall in the Late Miocene (Messinian), and only the reefs of the present-day Rowley Shoals (Mermaid, Clerke and Imperieuse reefs, as well as a drowned shoal to the southwest of Imperieuse Reef) continued to grow after this event. Growth of the Rowley Shoals reefs continued to keep pace with Pliocene-Recent sea-level changes, whereas the surrounding shelf subsided to depths of 230–440 m. We conclude that initial reef growth in the Rowley Shoals region was controlled by transpressional reactivation and structuring of the Mermaid Fault Zone during the early stage of collision between the Australian and Eurasian plates. During this structural reactivation, seabed fault scarps and topographic highs likely provided ideal sites for the initiation of reef growth. The subsequent growth and selective demise of the reefs was controlled by the interplay of eustatic sea-level variations and differential subsidence resulting from continued structural reactivation of the Mermaid Fault Zone. In contrast to models proposed in other regions, there is no direct evidence that active or palaeo hydrocarbon seepage triggered or controlled growth of the Rowley Shoals reefs or their buried Miocene predecessors.

This paper describes the relative influence of (i) landscape scale environmental and hydrological factors, (ii) local scale environmental conditions including recent flow history, and (iii) spatial effects (proximity of sites to one another), on the spatial and temporal variation in local freshwater fish assemblages in the Mary River, south-eastern Queensland, Australia. Using canonical correspondence analysis, each of the three sets of variables explained similar amounts of variation in fish assemblages (ranging from 44 to 52%). Variation in fish assemblages was partitioned into eight unique components: pure environmental, pure spatial, pure temporal, spatially structured environmental variation, temporally structured environmental variation, spatially structured temporal variation, the combined spatial/temporal component of environmental variation and unexplained variation. The total variation explained by these components was 65%. The combined spatial/temporal/environmental component explained the largest component (30%) of the total variation in fish assemblages, whereas pure environmental (6%), temporal (9%) and spatial (2%) effects were relatively unimportant. The high degree of intercorrelation between the three different groups of explanatory variables indicates that our understanding of the importance to fish assemblages of hydrological variation (often highlighted as the major structuring force in river systems) is dependent on the environmental context in which this role is examined.