SUMMARY1. Stream ecosystem health monitoring and reporting need to be developed in the context of an adaptive process that is clearly linked to identified values and objectives, is informed by rigorous science, guides management actions and is responsive to changing perceptions and values of stakeholders. To be effective, monitoring programmes also need to be underpinned by an understanding of the probable causal factors that influence the condition or health of important environmental assets and values. This is often difficult in stream and river ecosystems where multiple stressors, acting at different spatial and temporal scales, interact to affect water quality, biodiversity and ecosystem processes. 2. In this article, we describe the development of a freshwater monitoring programme in South East Queensland, Australia, and how this has been used to report on ecosystem health at a regional scale and to guide investments in catchment protection and rehabilitation. We also discuss some of the emerging science needs to identify the appropriate scale and spatial arrangement of rehabilitation to maximise river ecosystem health outcomes and, at the same time, derive other benefits downstream.3. An objective process was used to identify potential indicators of stream ecosystem health and then test these across a known catchment land-use disturbance gradient. From the 75 indicators initially tested, 22 from five indicator groups (water quality, ecosystem metabolism, nutrient cycling, invertebrates and fish) responded strongly to the disturbance gradient, and 16 were subsequently recommended for inclusion in the monitoring programme. The freshwater monitoring programme was implemented in 2002, funded by local and State government authorities, and currently involves the assessment of over 120 sites, twice per year. This information, together with data from a similar programme on the region's estuarine and coastal marine waters, forms the basis of an annual report card that is presented in a public ceremony to local politicians and the broader community. 4. Several key lessons from the SEQ Healthy Waterways Programme are likely to be transferable to other regional programmes aimed at improving aquatic ecosystem health, including the importance of a shared common vision, the involvement of committed individuals, a cooperative approach, the need for defensible science and effective communication. 5. Thematic implications: this study highlights the use of conceptual models and objective testing of potential indicators against a known disturbance gradient to develop a freshwater ecosystem health monitoring programme that can diagnose the probable causes of degradation from multiple stressors and identify the appropriate spatial scale for rehabilitation or protection. This approach can lead to more targeted management investments in catchment protection and rehabilitation, greater public confidence that limited funds are being well spent and better outcomes for stream and river ecosystem health.

Here, we relate the ongoing taxonomic story of a species complex of problematic, cryptic Australian freshwater shrimp (Atyidae; Caridina) to highlight the relative strength and utility of different taxonomic methods in assessing species boundaries. We used popular 'DNA barcode' gene fragments cytochrome c oxidase 1 and 16S ribosomal DNA. We then assessed the morphological attributes of these specimens and developed an identification key to complement the molecular results, and conclude that, despite occasionally strident arguments in favour of either molecular or morphological taxonomy, the two are inseparably linked and form parts of a greater whole.

Dry river beds are common worldwide and are rapidly increasing in extent due to the effects of water management and prolonged drought periods due to climate change. While attention has been given to the responses of aquatic invertebrates to drying rivers, few studies exist on the terrestrial invertebrates colonizing dry river beds. Dry river beds are physically harsh and they often differ substantially in substrate, topography, microclimate and inundation frequency from adjacent riparian zones. Given these differences, we predicted that dry river beds provide a unique habitat for terrestrial invertebrates, and that their assemblage composition differs from that in adjacent riparian zones. Dry river beds and riparian zones in Australia and Italy were sampled for terrestrial invertebrates with pitfall traps. Sites differed in substrate type, climate and flow regime. Dry river beds contained diverse invertebrate assemblages and their composition was consistently different from adjacent riparian zones, irrespective of substrate, climate or hydrology. Although some taxa were shared between dry river beds and riparian zones, 66 of 320 taxa occurred only in dry river beds. Differences were due to species turnover, rather than shifts in abundance, indicating that dry river bed assemblages are not simply subsets of riparian assemblages. Some spatial patterns in invertebrate assemblages were associated with environmental variables (irrespective of habitat type), but these associations were statistically weak. We suggest that dry river beds are unique habitats in their own right. We discuss potential human stressors and management issues regarding dry river beds and provide recommendations for future research.

Waterholes within the dryland Cooper Creek, Lake Eyre Basin, Australia, are connected only during floods and are typically isolated for long periods. Spatial changes in the macroinvertebrate assemblages of 15 of these waterholes belonging to four regions were explored and these changes were related to environmental aspects of the waterholes measured at four spatial scales: floodplain, waterhole, within waterhole and sample habitat. To explore temporal patterns, one region was sampled on four occasions differing in time since connection. Spatial patterns were characterised by ‘differentiation by distance’ whereby samples collected closer to each other in the landscape were more similar in assemblage composition than those collected further apart. Thus, there were significant differences between the assemblages of the four regions. Although there was a correlation between macroinvertebrate spatial patterns and a combination of local habitat, geomorphology and water chemistry attributes, it appears unlikely that these variables were responsible for the faunal differentiation by distance. Temporal variability was larger than spatial variability and temporal assemblage patterns were best explained by the ‘connectivity potential’ of waterholes, reflecting the position of individual waterholes within the broader channel network and long-term connectivity relationships, rather than the actual time since hydrological connection.

Salinity is a key abiotic property of inland waters; it has a major influence on biotic communities and is affected by many natural and anthropogenic processes. Salinity of inland waters tends to increase with aridity, and biota of inland waters may have evolved greater salt tolerance in more arid regions. Here we compare the sensitivity of stream macroinvertebrate species to salinity from a relatively wet region in France (Lorraine and Brittany) to that in three relatively arid regions eastern Australia (Victoria, Queensland and Tasmania), South Africa (south-east of the Eastern Cape Province) and Israel using the identical experimental method in all locations. The species whose salinity tolerance was tested, were somewhat more salt tolerant in eastern Australia and South Africa than France, with those in Israel being intermediate. However, by far the greatest source of variation in species sensitivity was between taxonomic groups (Order and Class) and not between the regions. We used a Bayesian statistical model to estimate the species sensitivity distributions (SSDs) for salinity in eastern Australia and France adjusting for the assemblages of species in these regions. The assemblage in France was slightly more salinity sensitive than that in eastern Australia. We therefore suggest that regional salinity sensitivity is therefore likely to depend most on the taxonomic composition of respective macroinvertebrate assemblages. On this basis it would be possible to screen rivers globally for risk from salinisation.