Rivers often span administrative boundaries, and their condition may be best protected and managed under national policies, supported by coordinated national bioassessment. To improve bioassessment practice in Australia we recommend: (1) convene a summit of policy makers and key scientists; (2) develop strategies and priorities to protect rivers and meet emerging challenges; (3) identify key biological indicators; (4) establish measures of success; and (5) develop plans for both ‘bottom-up’ community-driven bioassessment and ‘top-down’ government-led programs.

Dams, weirs and other barriers disrupt river connectivity and degrade fish communities worldwide. Fishways are in place at few sites relative to the numbers of barriers, and very few effectively mitigate barrier effects. Herein we review migratory behaviour among Australian fish and the effects of fish passage barriers. Australia’s highly variable hydrology challenges mitigation programs; options include basin-scale approaches; improved management of barriers, environmental flows and water quality; barrier removal; and development of improved fishway designs.

Data from the Murray–Darling Basin Authority’s Sustainable Rivers Audit were used to classify the Murray–Darling Basin into nine regions with similar historical fish assemblages. We demonstrate how a regionalisation framework can be useful for characterising fish communities and providing a baseline for assessing change in species assemblages.

Ephemeral rivers in northern Australia break up into a series of waterholes during the dry season, within which fish have to survive. This depends on the waterholes lasting throughout the dry season and with temperatures that are not lethal. Using comprehensive waterhole temperature data, we found that fish could survive in waterholes that remained deeper than 0.5 m, especially if they were turbid.

Deep pools of intermittent rivers in semi-arid regions provide refuge for aquatic biota during no flow periods. Pool depth is critical because it controls how long pools persist between flows. This study examines sedimentation rates in deep pools of intermittent rivers in eastern Australia to determine if rates have increased since European settlement and if depth reductions arising from higher rates reduce pool persistence times. Results show sedimentation has increased substantially and reduced persistence times by several months.

The choice of survey method can influence both the effectiveness and efficiency of monitoring programs. The present paper compares six commonly employed survey methods for six species of frogs and their tadpoles. Each survey method differed with respect to the probability of detection and the number of surveys required to determine the species.

The dusky spinefoot (Siganus luridus) entered the Mediterranean through the Suez Canal, conquering the eastern sectors of the basin, with marked effects on both natural habitats and native communities. In this study we monitored a recent population of this tropical invader, which settled around the island of Linosa in 2003. The results show how the invasion had expanded to the west, with increasing abundance at the invasion front.

Teleost spatiotemporal distributions and key abiotic associations were quantified throughout an important estuary within Brazil’s Atlantic Forest biosphere. As in other subtropical estuaries around the world, assemblages mostly comprised juveniles. Five species dominated samples, and their distributions were either negatively affected by salinity or positively affected by temperature or depth. These patterns were attributed to species-specific life stage requirements, and ultimately support clear conservation strategies.

Incorporating species trait information may provide insight into complex trophic interactions. In this study, we evaluated the effect of the common carp, Cyprinus carpio, on aquatic ecosystems, focusing particularly on middle-out-mediated effects. Common carp foraging activities and abiotic effects caused a shift in ecosystem structure and function. Specific autecology information will be critical for understanding the effects of ecosystem engineers and invasive species.

The present study provided evidence of interannual changes in the M. schmitti reproductive aggregation patterns in coastal waters of the south-western Atlantic Ocean, associated with different bottom-temperature regimens, depending on depth. The M. schmitti reproductive aggregations, observed during spring, were associated with temperatures above 16–17°C, which occurred mainly in shallow waters. The results suggested that changes in depth-dependent bottom-temperature patterns may be important drivers of the reproductive dynamics of this species.

Multi-generational exposure of oysters Saccostrea glomerata to acid sulfate soil runoff altered predator–prey interactions between the oysters and mud crabs Scylla serrata. Mud crab predation was greater on oysters from reference sites than affected sites, and the time mud crabs spent foraging was positively correlated with oyster mortality, providing a potential mechanism for observed trends in oyster mortality.

The invasive apple snail Pomacea canaliculata feeds primarily on aquatic plants, but some anecdotal reports indicate that it also consumes carrion. Herein, we studied carrion ingestion and its effects on growth, concluding that carrion may be important as an alternative resource when aquatic plants are absent. This feeding flexibility helps explain the potential of P. canaliculata to establish in new wetlands and, paradoxically, its persistent effects on aquatic vegetation.

We examine the impacts of consecutive bleaching events in 2002 and 2003 on coral susceptibility across various habitats and depths at Moorea, French Polynesia. Bleaching effects were genus specific and highly variable at small spatial scales. This variability has important implications for assessing changes to coral community structure over time and for estimating coral-reef resistance and resilience to future bleaching disturbance.

In this paper, we tested the influence of species–area relationship and species–energy association on taxonomic richness and functional richness of fish assemblages of tropical streams. Using data of two distinct basins, we demonstrated that the influence of area and energy varies for each basin, a possible response to local conditions of the environment.

Juvenile penaeid prawns were sampled from temperate intertidal marsh and subtidal creeks. Very few prawns were sampled within the intertidal marsh, suggesting these habitats may generally not be directly utilised by juvenile penaeids in temperate Australia. Larger school prawns (M. macleayi) sampled from the middle of subtidal creeks compared to edge habitat. Although juvenile penaeids may not directly utilise intertidal marshes, they may still export important resources for prawns in subtidal creeks.

In aquatic systems, odour cues can be used to quickly identify predation risk. Here, we show temperate marine and tropical freshwater shrimp avoid predator odours but not those of non-predators or conspecifics. Cues also alter habitat selection, with structurally complex habitats favoured when predator odour is present. Rapidly altering behaviour in response to perceived risk could reduce predation while increasing time available for tasks such as foraging.

The cyanobacterium Aphanizomenon favaloroi was identified for the first time in Europe in the Mediterranean brackish Lake Vistonis during July–August 2014. During its occurrence, the cyanotoxins saxitoxin and neo-saxitoxin were detected in the lake, coinciding with a massive fish kill. This saxitoxin-producing species may pose a health risk to animals and humans and have adverse effects on water quality.