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Reservoirs are intermediate ecosystems between rivers and lakes. These ecosystems break up the landscape by forming artificial lakes connected by rivers and change important ecological processes of lotic ecosystems (e.g. organic matter production and nutrient cycling) and thus have direct effects on aquatic biodiversity. We test the hypothesis that damming water courses exerts a negative effect on the zooplankton community by decreasing the alpha diversity. Samplings were conducted in 30 reservoirs and 29 natural lakes in the Neotropics, during two hydrological periods (dry and rainy) in 2001. The study analysed differences in alpha diversity, the number of rare, accessory and constant species, and species composition between the types of lakes. Alpha diversity was significantly higher in natural lakes and species composition differed between natural lakes and reservoirs. Zooplankton alpha diversity was positively related to total phosphorus (best model), indicating that productive environments (natural lakes) gather more species. Our results suggest that reservoirs have negative effect on community structure, whereas natural lakes have an important ecological function for biodiversity conservation because they are refuges for biodiversity.

Cephalopods are sensitive to environmental conditions due to their fast growth rates and short life cycles, being thus considered good ecological indicators. Here, we analyzed western Mediterranean cephalopod paralarvae communities during two consecutive summers (2004 and 2005) characterized by contrasting oceanographic conditions. Our main aim was to determine to what extent such contrasting scenarios affected the spatial distribution of the cephalopod early life stages and decipher the main environmental factors affecting each particular taxon. The contrasting oceanographic conditions during 2004 and 2005 included differences in the shape and location of a regional frontal system, which brought about differences in the sea circulation and the temperature regime. Such contrasting scenarios were reflected in the spatial distribution and the frequencies of appearance of both the whole community and the individual taxa. There was not any major factor affecting most taxa equally, which points to differences in species sensitivity to external conditions. Moreover, our results evidenced that paralarvae populations were more influenced by regional sea salinity and temperature than by mesoscale hydrographic features. Our study reveals that moderate changes in sea temperature have a major effect on the presence of paralarvae populations, which has profound implications in the context of the current global warming., SI

Fish-based multi-metric indices are an integral tool in implementing effective water policy initiatives for transitional waters. This study analysed the behaviour of three fish indices (TFCI in the UK, ELFI in France and EFAI in Portugal) developed for monitoring in line with the European Water Framework Directive, by applying a supervised multi-way sensitivity analysis with national monitoring data. The relative variation in the index outcome was analysed under different simulation scenarios by setting metric values at various levels and accounting for the co-variation between metrics. Subsets of key metrics were identified based on their higher influence in determining the index output. Index results under manipulations of metric scores clearly indicated that metric type, number of metrics used and correlations between metrics are important in determining their behaviour. This has implications for implementing management/conservation plans, for example, by prioritising restoration and/or conservation of metrics influencing more the ecological status. Indices including uncorrelated metrics (e.g. EFAI) or metrics with a skewed distribution (e.g. TFCI) are less affected by extreme metric changes, reducing the effectiveness of management actions aimed at improving the ecological status of a water body and thus adjustments may be needed to increase their sensitivity to changes in their metrics.

The EU’s Water Framework Directive (WFD) in particular makes good use of riverine biota—including fish—as ecological indicators of river integrity. However, it is also important to examine when our indicators fail to serve the purpose for which they were originally intended: to consistently and reliably describe the quality of the environment. We argue that in the Czech Republic (and probably several other European countries), the use of adult fish as ecological indicators often fails to fulfill these purposes for several reasons, especially when fish are stocked in natural waters, for practical considerations during field sampling, and problems with public relations. The ecological quality of running waters sensu WFD is usually assessed on the basis of the adult fish assemblage. The aim of this study is to describe disadvantages of monitoring river integrity using adult fish in Czech Republic, which has regular and widespread stocking of more than one-third of fish species present in running waters and to suggest the alternative strategy of young-of-the-year (YOY) fish monitoring for assessing river ecological quality with the ability to provide a sensitive response to water quality and habitat structure regardless of the effect of stocking or river size. We conclude that even though YOY sampling is often a more logical and practical approach to water quality monitoring under specific conditions, no method is perfect and caution should be taken. For example, YOY can have high annual variability in density and higher sensitivity to summer flood events than adults. The suitable time for sampling YOY fishes in late summer is much shorter than for the adult fish community, and therefore must be considered when designing a successful monitoring strategy. Monitoring of YOY fishes does not provide direct information about age structure of fish populations, which is required by WFD. YOY sampling is a useful—albeit imperfect—method for providing a sensitive response to ecological status of rivers, especially under specific stocking conditions.

This study investigated the fish fauna of a stream in southeastern Brazil that runs through sugar cane-growing and urban areas that are subject to sewage discharge. It aimed to determine the importance of spatial and environmental factors on fish distributions and to assess the use of fish as indicators of the environmental conditions. A longitudinal pattern of chemical water quality was observed, with more disturbed conditions at the urban sites. Several opportunistic or tolerant and omnivorous species such as Astyanax altiparanae, Poecilia reticulata, and Astyanax fasciatus were numerically abundant at these urban sites, which resulted in a consistent increase in species density and biomass along the stream. Redundancy analysis extracted three axes, identifying a nutrient–productivity gradient associated with different species composition patterns, as also detected by the indicator species analysis. No species could be considered a potential indicator of the agricultural area in the dry season, whereas four different species were judged potential indicators of three urban sites. In order to explain species distribution, variation in species abundance was partitioned into spatial and environmental components. The latter was more important, explaining 25.4% of the variation. We concluded that the fish assemblage of the Guamium stream is undergoing the initial stages of disturbance, with pronounced effects at the urbanized area, but no detectable changes at the sugar cane sites. Therefore, fish assemblages might be used as ecological indicators to detect urban impacts in similar rivers. However, the potential use of fish to diagnose stressors in areas of sugar cane plantations should be complementary to more comprehensive studies aimed at understanding the influence of this crop on freshwater resources.

In accordance with the Water Framework Directive guidelines (WFD, 2000, European Communities Official Journal L327 2000/60/EC), classification schemes and ecological evaluation tools (based on benthic invertebrate fauna data sets from 1990 to 2002) were applied in the lower Mondego estuary. Two distinct scenarios could be tested due to the implementation of mitigation practices in 1999, following a long eutrophication process, which started by the early 1980s. Some discrepancies in the results were found by the application of the different indices. The AMBI index (accounting for taxonomic composition) and the ABC method (accounting for abundance and biomass k-dominance patterns) classifications often disagreed with those based on species diversity (Margalef and Shannon-Wiener). The ambiguous results made the classification a complex task to achieve, contrary to the Directive’s objective of maintaining it simple and clear. Our results suggest the necessity of adjusting some of the indices and their ranges to estuarine characteristics, namely to account the typical dominance and abundance of some particular species. These aspects are not taken into consideration by some of the indices proposed, which are more adapted to typical marine conditions. Based on our results, these widely applied indices might still improve their efficiency in estuarine systems allowing their use in the resembling types already established within the new Directive agenda.

During low water levels, habitats in river-floodplain systems are isolated from each other and from the main river. Oppositely, floods tend to connect water bodies with distinct hydrological characteristics and, as a result, ecological processes and biological communities tend to be more similar among the distinct habitats that comprise a river-floodplain system. Based on a literature review and also using unpublished data obtained in tropical floodplains, the aim of this paper is to highlight the effects of floods as a process that reduce spatial variability. The usual negative relationship between the coefficient of variation of any ecological indicator (e.g., chlorophyll-a or total phosphorus) and water level is the main result demonstrating a reduction in spatial variability due to floods. Considering physical, chemical or biotic data gathered in distinct habitats within the floodplain, this pattern was found in temperate and tropical regions, subjected to distinct levels of anthropogenic impacts, and at different spatial extents. The main mechanism that accounts for this pattern may be stated as follow. During low water level, the biological communities of each habitat in the floodplain (e.g. lagoons, backwater, streams) follow distinct temporal trajectories due to the effects of local driving forces (e.g. an efficient predator trapped in a lagoon but not in another). Management plans and biodiversity conservation in river floodplain systems will benefit by considering the effects of flood homogenization and increased connectivity peculiar to these unique ecosystems.

Successful stream restoration requires the setting of appropriate goals and an ability to measure restoration success using quantitative ecological indicators. At present, a dichotomy exists between the setting of restoration goals to enhance ecosystem ‘processes’ or ‘functions’ such as sustainability, and measuring the success of these goals using ‘patterns’ or ‘structural’ ecosystem attributes. The presence of a structural facade may be no indication of a viable ecosystem as this requires evaluation of whether key ecosystem processes have been restored and whether the system is ecologically sustainable. We briefly discuss the benefits and drawbacks associated with setting restoration goals and measuring their success based on ecosystem patterns and processes. Two case studies are provided based on measurements of biofilm chlorophyll a and Dissolved Organic Carbon (DOC) to debunk the myth that these structural variables can be used as surrogates for ecosystem processes of productivity and respiration in rivers. We suggest that the discipline of restoration ecology will benefit and grow from a greater appreciation of the functional role of biological communities within stream ecosystems, and from targeting some restoration towards the re-establishment of structurally significant species and functionally significant processes. This approach to stream restoration with a well-founded conceptual base and defined scientific and management goals should expand our knowledge of stream function and contribute to the effective restoration of stream systems.

Dryland rivers occur over much of Australia's inland and have some of the most variable patterns of flow in the world. Despite their dominance in terms of Australia's river types, dryland rivers have not been the focus of the recent increase in research on indicators of river health, mostly owing to their spatial remoteness and relatively low levels of water resource development and human disturbance. Most rivers in arid and semi-arid regions are ephemeral, and only carry significant flows during the wetter months or following infrequent but intense rainfall events. It is not known which, if any, of the existing approaches to river health assessment can be used to accurately assess the health of these large ephemeral rivers. This paper considers why the standard methods for interpreting the currently-used indicators for river health may need to be adapted for variable systems and suggests the use of trends that recognise natural variation in indicator values for undertaking this.

Ecosystem health is a newly proposed concept that sets new goals for environmental management. Its definition, indexing and assessment methods are still being perfected. An Ecological Modeling Method (EMM) for lake ecosystem health assessment is proposed in this paper. The EMM's procedures are: (1) to analyze the ecosystem structure of a lake in order to determine the structure and complexity of the lake's ecological model; (2) to develop a model having ecological health indicators, by designing a conceptual diagram, establishing model equations, estimating model parameters and being integrated with ecological indicators; (3) to compare the simulated and observed values of important state variables and process rates (i.e. model calibration) in order to evaluate the applicability of the model to lake ecosystem health assessment; (4) to calculate ecosystem health indicators based on the developed model; and (5) to assess lake ecosystem health according to the values of the ecosystem health indicators. The EMM was applied, as a case study, to the ecosystem health assessment of a eutrophic Chinese lake (Lake Chao) between April 1987 and March 1988. A relative order of health states from poor to good was determined as follows: August–October 1987 > April–May 1987 > June–July 1987 > November–December 1987 > January–March 1988. These results compared quite favourably with the actual current conditions at Lake Chao. The EMM method, therefore, was suitable in assessing lake ecosystem health at Lake Chao.

Evaluating ecological responses to restoration is important for assessing the success of river restorations. We evaluated the response of species richness and diversity of aquatic macrophyte (hydrophyte, instream aquatic plant) growth forms and strategies (Grime’s CSR strategies; C competitive, S stress tolerant, R ruderal) in 10 small- and 10 large-scale river restoration projects in nine European countries. Restoration had no effect on total richness and diversity but significant effects if specific growth forms and plant strategies were considered. Results indicated that restoration caused an increase in the richness and diversity of submerged and a decrease in the proportion of competitive species. Responses were especially pronounced in relatively small widening projects in gravel-bed mountain rivers but not in relatively large restoration projects in sand-bed lowland rivers. Moreover, flow restoration increased the richness and diversity of floating-leaved species. In rivers with a high proportion of wetlands and waterbodies in the catchment, restoration increased the abundance of competitive plants. These results highlight that river and catchment properties need to be considered when evaluating river restoration projects. We suggest hydrophyte growth forms and plant strategies as suitable response variables to assess the effect of river restoration projects.