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We argue for improved conservation of freshwater ecosystems at catchment or eco-regional scales by explicit assignment of values to all river sections and wetlands, recognising current disturbance, and aiming for ‘no further harm’ to the commons. The need is indicated by the global deterioration of biodiversity and ecosystem services of rivers and wetlands, increasing demands on water and land resources, and climate change. Regional pressures include multiple jurisdictions, competing demands, piecemeal management, pollution and habitat impacts. Effective resource and conservation management needs to integrate multiple uses via governance of activities of stakeholders, recognising hydrogeomorphic, water quality and ecological properties of ecosystems. Complete ecological protection is impractical amidst water-resource and land-use development, but we suggest that all river reaches and wetlands be given a conservation rating based on habitat, biodiversity and connectivity values. We present a straightforward approach to spatial conservation rating of freshwaters, using hydrogeomorphic typology and assignment of conservation values on the basis of available information and expert elicitation. We illustrate the approach by using the large Burdekin River catchment in north-eastern Australia. This approach is complementary to more spatially focused conservation prioritisation and could greatly improve management for sustainability, reduce further decline in conservation values, and facilitate rehabilitation.

There is limited information available on the ecology of planktonic invertebrate assemblages of small tropical lowland rivers, despite zooplankton being a vital resource for larval fish. Herein we describe the spatial patterns and temporal dynamics of invertebrate zooplankton at 8 locations over a 25-month period in the lowland section of a short coastal river in the Australian Wet Tropics. Zooplankton were more abundant in slack than flowing waters and assemblages were dominated by Copepoda, but contained many less numerous taxa, including freshwater invertebrates at the more upstream sites. Taxonomic richness, total density and the densities of the most abundant taxa were greatest in the most downstream sites. Seasonal patterns in the density of zooplankton did not differ between the 2 years. Distance-based linear modelling of assemblages identified distance downstream and associated variables, such as salinity, as the most important environmental effects on zooplankton. The zooplankton assemblage in the lower Mulgrave River is strongly influenced by the incised nature of the river, perennial flows, the presence of slack waters, wet season floods and estuarine incursion. Zooplankton dynamics differ from the typical pattern of tropical floodplain systems in that their maximum proliferation occurs during the benign but productive late dry season.

Waterholes that remain in the dry season in intermittent dryland rivers are important biotic refugia, but detailed ecological descriptions of these habitats and their plankton are scarce. We aimed to determine spatial and temporal variation in phytoplankton assemblages in a tropical Australian dryland river system, their main environmental determinants and the potential of the phytoplankton for ecosystem monitoring. We sampled nine sites in three rivers over 2 years using standard methods. Water quality and phytoplankton assemblages varied considerably among sites, rivers and seasons, reflecting lithology, hydrology, bathymetry and local catchment influences. Major environmental drivers included conductivity, pH, temperature and species of N and P. We analysed several derived versions of the original dataset by using density and presence–absence data, eliminating rarer species and grouping species into higher taxa. We found substantial consistency among analyses in environmental drivers, identified using distance-based linear modelling, and in variability among systems, identified using nested permutational multivariate analysis of variance (PERMANOVA). Responsiveness of the algal assemblages to environmental drivers and consistency among analyses, even using subsamples at low taxonomic resolution, suggests potential for ecosystem monitoring and optimising of sample throughput, although variability among systems requires substantial effort to determine the range of reference conditions.

We identified influences of land-use disturbances on invertebrate assemblages in streams draining eight areas of the Great Barrier Reef catchment in tropical Australia (~15.7–22°S), a region of high biodiversity. We used distance-based linear modelling (DistLM) to analyse assemblage data (103 taxa), richness and the SIGNAL2 taxon sensitivity index. DistLM of assemblages explained ~40% of variation across all samples and 7–54% of variation in individual areas. DistLM of richness and SIGNAL2 explained respectively 19–81 and 26–95% of variation. Explanatory variables were land use (especially cropping and grazing v. forest), riparian width, instream habitat, climate (drier south) and water quality (conductivity greater in south). Local impacts of activities such as mining were evident in models of individual areas. A detailed comparison of streams with contrasting riparian management demonstrated a 25% loss of richness, but no change in SIGNAL2 score. Accounting for local environmental gradients and using measures appropriate to the type of disturbance improved identification of impacts, and could form a framework for future regional monitoring of stream ecological condition. The impacts identified may be mitigated by remediation such as riparian rehabilitation, although management at catchment scales is required to be effective.

Hypoxia can profoundly affect fish reproduction and larval development, but its effects on fish from tropical Australia are not well understood. In the present study, the effects of diel fluctuating hypoxia on reproduction and embryo viability were investigated for a range-limited tropical freshwater fish, namely the Utchee Creek rainbowfish (Melanotaenia utcheensis). The lethal level for adult rainbowfish after gradual oxygen depletion was ~7% dissolved oxygen (DO) saturation. After 28 days, the reproductive success of adult fish exposed to fluctuating hypoxia treatments was measured by fecundity, gonad health, egg incubation time, egg and larval mortality, viability and size of hatching larvae. Reproduction was impaired in the lowest sublethal treatment (minimum 10% DO saturation each day). No ill effects of parental exposure to diel fluctuating hypoxia on embryos were identified, and minor differences in temperature between aquaria had a greater effect on embryos than parental hypoxia treatments. Similarly, no effects of embryonic exposure to diel fluctuating hypoxia were identified. Utchee Creek rainbowfish appear to be more hypoxia tolerant than temperate species, in keeping with their habitat in warm lowland streams, but they are still susceptible to the increasing frequency and intensity of hypoxia possible with increasing temperature and reduced flow as a result of climate change.

Hypoxia can have profound sublethal effects on reproduction and embryonic development of some freshwater fish. In the present study, the effects of diel fluctuating hypoxia on embryo viability were investigated for the eastern rainbowfish Melanotaenia splendida splendida, a small-bodied species common in wetlands of tropical Queensland. After daily hypoxic exposure (minimum 5% saturation) from fertilisation until hatch, no effects were found on egg incubation time, egg and larval mortality, and viability and size of hatching larvae. Older life history stages of the species are vulnerable to this level of hypoxia. Embryos of phytolithophilic species are likely exposed to fluctuating dissolved oxygen saturations in their natural habitat, and hypoxia tolerance may be a requirement for fish species that spawn predominantly on submerged plant material.

Adequate conceptual frameworks that link land use to water quality and ecosystem health are lacking for tropical and subtropical freshwater systems, so we review here extensive water-quality research undertaken in the Great Barrier Reef catchment area (GBRCA) and present conceptual models synthesising the dynamics of agricultural pollutants and their ecological effects. The seasonal flow regime defines the following key periods of water-quality risk over the annual hydrological cycle for diverse GBRCA ecosystems: initial ‘pre-flush’ flows during the transition from the dry to the wet season; early wet-season ‘first flush’ flows; peak wet-season flood flows; and sustained base flow or periods of disconnection during the dry season. The level of seasonal contrast varies from the perennial systems of the wet tropics to the intermittent systems of the dry tropics. Major water-quality stressors may be catchment scale (e.g. in streams draining broad-scale agriculture) or more localised (e.g. cattle access, irrigation tail water). Water-quality stressors such as ammonia toxicity and hypoxia (due to organic or nutrient run-off and enhanced plant productivity) are of low relevance to downstream GBR ecosystems but are major threats to fresh waters. Similarly, whereas high contaminant loads in wet-season floods present the highest water-quality risk to marine ecosystems, the greatest risk in fresh waters is often from acute contamination during early wet-season ‘pre-flush’ flows into lentic waters, or continuous input of contaminants over long periods of base flow. Because of differences in the nature of risk periods, water-quality threats and pollutant-delivery mechanisms, the benefits of different management options to improve water quality can also differ among freshwater habitats and between freshwater and marine environments.

Floodplain lagoons in the Queensland Wet Tropics bioregion, Australia, are important and threatened habitats for fish. As part of studies to assess their ecological condition and functions, we examined patterns of occurrence of fish larvae, juveniles and adults in 10 permanent lagoons on the Tully–Murray floodplain. Lagoons contained early life-history stages of 15 of the 21 native species present, including 11 species that complete their life cycle in fresh waters and 4 that require access to saline habitats for larval development. Lagoon connectivity to the rivers, distance from the coast and flood dynamics influenced temporal variation in fish abundance, population size structures and recruitment patterns. This study and the literature show that wet, post-wet and dry-season habitats are utilised by small opportunists (e.g. Melanotaenia splendida), an equilibrium species (Glossamia aprion) and larger periodic strategists (neosilurid catfishes). Maintenance of natural seasonal patterns of flow and connectivity, and active protection of permanent floodplain lagoons from riparian and land-use disturbance, will be essential if their roles in fish recruitment are to be sustained.

Hypoxia in freshwater ecosystems of the Australian wet tropics occurs naturally, but is increasing as a result of anthropogenic influences. Diel cycling of dissolved oxygen (DO) concentration (fluctuating hypoxia) is common in the region. Laboratory experiments sought to identify relationships between severity of fluctuating hypoxia and sublethal effects on ventilation, feeding and growth for juvenile barramundi (Lates calcarifer), eastern rainbowfish (Melanotaenia splendida splendida) and sooty grunter (Hephaestus fuliginosus). Fish continued to feed and grow under daily exposure to severe fluctuating hypoxia treatments for several weeks. Ventilation rates increased in a significant direct quadratic relationship with the severity of hypoxia treatments and increasing hypoxia caused ventilatory behaviour changes in all species. Barramundi and rainbowfish attempted aquatic surface respiration and were more tolerant of severe hypoxia than was sooty grunter; barramundi and rainbowfish are also more likely to experience hypoxia in the wild. There was a significant quadratic relationship between growth and minimum DO saturation for barramundi. Although all three species were tolerant of hypoxia, anthropogenic stressors on tropical Australian aquatic ecosystems may increase the frequency and severity of hypoxic conditions causing a concomitant increase in fish kill events.

We investigated the biophysical environment, invertebrate fauna and ecosystem health of lagoons on the Tully–Murray floodplain in the Queensland Wet Tropics bioregion. These wetlands are biologically rich but have declined in area and condition with agricultural development and are poorly protected, despite being located between two World Heritage areas. Lagoons varied in size, habitats and water quality, with increasing signatures of agriculture (e.g. elevated nutrient concentrations) from the upper to lower floodplain. Zooplankton were abundant, but not diverse, and correlated variously with environmental variables, so were not useful in assessing lagoon condition. Benthic macroinvertebrates were abundant and diverse and correlated strongly with riparian condition, habitats, water quality and degree of agriculture in the catchment, but gradients in assemblage structure were not strong because the flow regime, with multiple annual floods, maintains higher water quality than in some tropical systems. The absence of pristine reference lagoons and the limited availability of replicate sites hamper the development of monitoring systems. Nevertheless, we show that appropriate sampling, analysis and knowledge of comparable systems allow inferences to be drawn regarding ecological condition. This is important because environmental managers need best available and timely advice whatever the opportunities for rigorous study design.

In freshwater systems, dissolved oxygen (DO) saturation frequently fluctuates, falling at night and rising during the day in response to respiration and photosynthesis, respectively, of aquatic biota. Low DO (hypoxia) is a common cause of fish kills in freshwater systems around the world. Laboratory studies on responses of fish to fluctuating DO are currently limited, and require techniques that produce a realistic cycle of DO depletion and replacement. Artificial DO-depletion mechanisms frequently used for hypoxia studies may underestimate the field effects of hypoxia on fish because of the lack of the naturally occurring synergistic effect of lower pH, and seldom allow fish to employ behavioural adaptations to hypoxia, such as aquatic surface respiration. We demonstrate proof-of-principle for an alternative method of creating fluctuating hypoxia in an experimental environment, using the natural rhythms of photosynthesis and respiration of aquatic plants to create realistic conditions. A range of volumes of aquatic macrophytes were used alone and in combination with fish to lower DO saturation in sealed freshwater aquaria, and achieved DO saturations as low as 1.3%. This cost-effective method can be deployed over long periods with minimal effort in comparison to traditional methods of DO reduction.

With the covariation between fish form and function of long-standing interest to fish biologists, ecomorphological research provides a framework for assessing the interaction between the morphology of an organism and their ecology. Whereas ecomorphological studies of Australian fishes are rare, the terapontid grunters are an ideal candidate for study because of their diversity of dietary habits. We examined the morphological correlates of the diet of 21 species of northern Australia’s terapontids and their constituent ontogenetic trophic units. Preliminary analyses focusing on morphology identified the role of allometric growth – in characters such as intestinal length, maxilla length and mouth width – as driving considerable ontogenetic divergence in interspecific morphological trajectories. A significant relationship was identified between diet and morphology across species, although morphology explained only half of the observed dietary variation. Body size, and its relationship to allometric development of several morphological parameters, appears to constrain the trophic habits expressed by many terapontids at different life-history stages. Many of the diet–morphology relationships evident within the Terapontidae parallel those seen in other studies, providing substantial corroboration for the ecomorphological approach. This demonstrates that selective pressures have driven morphology in terapontids to converge morphologically with other ecologically comparable fishes across the globe.

In Australia’s Wet Tropics rivers, perennial base flows punctuated by wet season floods drive instream responses across a range of spatial and temporal scales. We combined gut-content and stable-isotope analyses to produce preliminary webs depicting trophic links between fish, their main prey items and basal productivity sources. We then used these webs to test the applicability of general food web principles developed in other tropical systems. Although a range of sources appeared to underpin fish productivity, a large portion of total energy transfer occurred through a subset of trophic links. Variability in food web structure was negatively correlated with spatial scale, being seasonally stable at river reaches and variable at smaller scales. Wet Tropics rivers are similar to those in other tropical areas, but exhibit some unique characteristics. Their high degree of channel incision improves longitudinal connectivity, thereby allowing fish to move between mesohabitats and target their preferred prey items, rather than shifting their diet as resources fluctuate. However, this also inhibits lateral connectivity and limits terrestrial energy inputs from beyond the littoral zone.

Wet-season flooding causes dietary shifts in tropical freshwater fish by regulating instream productivity, habitat structure and food availability. These dynamics have been comprehensively documented worldwide, but data are limited for Australia’s Wet Tropics rivers. The aim of the present study was to extend our earlier fish–habitat model for these systems by examining the role of trophic dynamics in determining fish assemblage composition. Chlorophyll a and phaeophytin concentrations, benthic and littoral invertebrates and fish were collected at four sites in the lower Mulgrave River under a range of flow conditions. Wet-season flooding caused significant reductions in instream productivity, whereas habitat disturbance reduced densities and abundances of littoral and benthic invertebrates. However, volumetric gut contents of 1360 fish, from 36 species, revealed seasonal shifts in guild membership by only two species, with fish moving between sites to target their preferred prey items – largely irrespective of differences in habitat structure. As a result, the food consumed by the fish community present at each site closely reflected the seasonal availability of food resources. The present paper questions whether fish community composition in small tropical rivers can be accurately predicted from habitat surrogates alone and encourages consideration of constraints imposed by the trophic dynamics and reproductive ecology of fish.

Strong relationships between seasonal flooding, instream habitat structure and fish assemblages have been well documented in large tropical rivers (e.g. the flood pulse concept). However, the mechanics of these relationships are likely to differ substantially in smaller coastal rivers, such as those in Costa Rica, south-east Brazil and Australia’s Wet Tropics. These systems typically feature steep upland streams with short, deeply incised lowland channels and poorly connected floodplains. This hypothesis was investigated by documenting spatial and temporal variation in fish-habitat relationships in the Mulgrave River, north-east Queensland. Sampling was conducted at four lowland sites under a range of flow conditions, from dry-season baseflows to a one-in-ten-year flood. Longitudinal environmental gradients and fine-scale habitat patches were important in regulating fish assemblage structure during the dry season. However, high wet-season flows, constrained by the deep channel, acted as disturbances rather than gentle flood-pulses. In particular, the mobilisation of bed sediments led to scouring of aquatic vegetation and a dramatic reduction in habitat heterogeneity. Seasonal movements of fish led to significant changes in assemblage structure – from a community dominated by Neosilurus ater, Hypseleotris compressa, Awaous acritosus and Redigobius bikolanus during the dry season, to one dominated by Nematalosa erebi, Ambassis agrammus and Glossamia aprion during the wet season. Based on these observations, together with information from the literature, a conceptual model of fish-habitat dynamics is presented that is better suited to small tropical rivers than those developed in larger systems with expansive floodplains.

The structure of stream communities is typically thought to be driven by stochastic events such as floods, in contrast with communities in many other systems in which biotic interactions have a major role. However, it is possible that biotic interactions are important in some situations in streams, especially where resources are limited and physical influences are stable for substantial periods. Leaf litter – the main energy source and a distinct habitat in forest streams – constitutes a patchy resource where biotic interactions among and within consumer species are likely to occur. The intraspecific interference in four leaf-eating species (shredders), common in Australian tropical streams, was experimentally examined – Anisocentropus kirramus (Trichoptera : Calamoceratidae), Lectrides varians and Triplectides gonetalus (Trichoptera : Leptoceridae) and Atalophlebia sp. (Ephemeroptera : Leptophlebiidae). All four species showed some degree of intraspecific interference, indicated by lowered leaf breakdown rates when density increased. Breakdown rates per capita decreased exponentially for all species with increased density, with slight differences among species. These differences were more evident when body size was taken into account, with breakdown rates depressed at lower densities for the two species with larger body sizes, T. gonetalus and Atalophlebia sp. Overall breakdown rates did not always increase with higher densities, because they were compensated for by depressed individual breakdown rates. Our results indicate that intraspecific interference can be an important mechanism regulating leaf breakdown in streams.

In temperate regions of the northern hemisphere, where stream thermal regimes fluctuate seasonally and predictably, temperature has a role in niche segregation and maintenance of patterns of lotic diversity and distribution, as described by the ‘Thermal Equilibrium Hypothesis’. In Australia, the role of temperature in regulating patterns of diversity and distribution has been obscure, as seasonal variation in stream temperatures can be exceeded by stochastic fluctuation in flow. The thermal responses of five lotic Chironomidae (Diptera) species, contrasting in biogeographic (evolutionary) history, from warm tropical and cool temperate Australian populations, were investigated. All species, including postulated cool-stenotherms, showed broadly eurythermic developmental and morphological responses, and maintained both survivorship and oocyte production at elevated temperatures despite reductions in overall body size. There were subtle differences among species according to biogeographic affinity, with tolerances of Gondwanan species, which were narrower than those of cosmopolitan species, best characterised as ‘mesothermic’, but there was little divergence between populations. These results have implications for the understanding of diversity and distribution of Australian chironomids, and indicate that applicability of the Thermal Equilibrium Hypothesis to Australian lotic faunas may be limited.

A method of preparing and interpreting the microstructure of otoliths of the eastern rainbowfish, Melanotaenia splendida splendida, was developed and used to validate the periodicity of increment formation. Otoliths were collected from laboratory-reared M. s. splendida of known age. The sagittal otolith was preferred for ageing because resolving the earliest increments was easier than in the lapillus during an early slow-growth period, up to 15 days after hatching. Increments formed in the sagittae before hatching, and a distinct discontinuity was visible in the otolith sections at a time corresponding to hatching. Another discontinuity occurred at the time of yolk-sac absorption, when larvae became completely reliant on exogenous feeding. After this, increments were clear, regularly spaced and easily resolved. Linear relationships were found between fish size and sagittal length, breadth and perimeter. Observations of the otolith sections confirmed that the increments in sagittae of M. s. splendida were laid down daily. The information provided here enables growth and mortality rates of M. s. splendida to be measured, providing a useful tool for monitoring the impacts of contaminants in tropical Australian waters.

This paper describes the ontogeny and morphogenesis of the eastern rainbowfish, Melanotaenia splendida splendida, including details on reproduction and the conditions required for laboratory breeding and rearing. M. s. splendida is easily bred under standard laboratory conditions using readily available commercial foods. Aquaria with two males and three females can produce between 40 and 200 eggs daily. They can be induced to spawn daily throughout the year through manipulation of light and temperature conditions. The eggs, which ranged in size from 0.93 to 1.20 mm, had a homogeneous yolk and a clear, uniform chorion, making observation of developmental stages possible. Development was telolecithical and division was meroblastic. Development of M. s. splendida was similar to that of other Melanotaenia species. At 28°C, hatching occurred between 4 and 8 days, with an average larval length of 3.7 mm standard length. Growth was rapid and the fish reached sexual maturity within approximately 90 days. Knowledge of the developmental stages of M. s. splendida is important in enabling further work, such as bioassays and environmental monitoring, to be carried out, investigating the ways in which changes in the environment, such as pollution, will impact on Australia's freshwater fishes. Melanotaenia splendida splendida is an ideal species for this purpose in the north-eastern tropics of Australia.