Long-term monitoring studies as a powerful tool in marine ecosystem research

The EU-funded research project WISER (“Water bodies in Europe: Integrative Systems to assess Ecological status and Recovery”) developed new assessment methods required by the EU Water Framework Directive (WFD) for lakes, coastal and transitional waters. WISER also addressed the recovery of biotic assemblages from degradation. The results are summarised in five key messages, supported by papers in this special issue and by WISER results published elsewhere: (1) Response to stress differs between organism groups, water types and stressors; a conceptual model is proposed summarising how the individual organism groups respond to different types of degradation in rivers, lakes, transitional and coastal waters. (2) The sources of uncertainty differ between BQEs and water types, leading to methodological suggestions on how to design WFD sampling programmes. (3) Results from about 300 current assessment methods indicate geographical variations in metrics but assessments are comparable at an aggregated level (“ecological status”). (4) Scale and time matter; restoration requires action at (sub)-basin levels and recovery may require decades. (5) Long-term trends require consideration; the effects of both degradation and restoration at the water body or river basin scales is increasingly superimposed by multiple stressors acting at large scales, in particular by climate change.     

The WISER metadatabase: the key to more than 100 ecological datasets from European rivers, lakes and coastal waters

In ecological sciences, the role of metadata (i.e. key information about a dataset) to make existing datasets visible and discoverable has become increasingly important. Within the EU-funded WISER project (Water bodies in Europe: Integrative Systems to assess Ecological status and Recovery), we designed a metadatabase to allow scientists to find the optimal data for their analyses. An online questionnaire helped to collect metadata from the data providers and an online query tool (http://www.wiser.eu/results/meta-database/) facilitated data evaluation. The WISER metadatabase currently holds information on 114 datasets (22 river, 71 lake, 1 general freshwater and 20 coastal/transitional datasets), which also can be accessed by external scientists. We evaluate if generally used metadata standards (e.g. Darwin Core, ISO 19115, CSDGM, EML) are suitable for such specific purposes as WISER and suggest at least the linkage with standard metadata fields. Furthermore, we discuss whether the simple metadata documentation is enough for others to reuse a dataset and why there is still reluctance to publish both metadata and primary research data (i.e. time and financial constraints, misuse of data, abandoning intellectual property rights). We emphasise that metadata publication has major advantages as it makes datasets detectable by other scientists and generally makes a scientist’s work more visible.     

REBECCA databases: experiences from compilation and analyses of monitoring data from 5,000 lakes in 20 European countries

Chemical and biological data from more than 5,000 lakes in 20 European countries have been compiled into databases within the EU project REBECCA. The project’s purpose was to provide scientific support for implementation of the EU Water Framework Directive (WFD). The databases contain the biological elements phytoplankton, macrophytes, macroinvertebrates and fish, together with relevant chemistry data and station information. The common database strategy has enabled project partners to perform analyses of chemical–biological relationships and to describe reference conditions for large geographic regions in Europe. This strategy has obvious benefits compared with single-country analyses: results will be more representative for larger European regions, and the statistical power and precision will be larger. The high number of samples within some regions has also enabled analysis of type-specific relationships for several lake types. These results are essential for the intercalibration of ecological assessment systems for lakes, as required by the WFD. However, the common database approach has also involved costs and limitations. The data process has been resource-demanding, and the requirements for a flexible database structure have made it less user-friendly for project partners. Moreover, there are considerable heterogeneities among datasets from different countries regarding sampling methods and taxonomic precision; this may reduce comparability of the data and increase the uncertainty of the results. This article gives an overview of the contents and functions of the REBECCA Lakes databases, and of our experiences from constructing and using the databases. We conclude with recommendations for compilation of environmental data for future international projects.     

A phytoplankton trophic index to assess the status of lakes for the Water Framework Directive

Despite improvements in wastewater treatment systems, the impact of anthropogenic nutrient sources remains a key issue for the management of European lakes. The Water Framework Directive (WFD) provides a mechanism through which progress can be made on this issue. The Directive requires a classification of the ecological status of phytoplankton, which includes an assessment of taxonomic composition. In this paper, we present a composition metric, the plankton trophic index, that was developed in the WISER EU FP7 project and demonstrate how it has been used to compare national phytoplankton classification systems in Northern and Central Europe. The metric was derived from summer phytoplankton data summarised by genus from 1,795 lakes, covering 20 European countries. We show that it is significantly related to total phosphorus concentrations, but that it is also sensitive to alkalinity, lake size and climatic variables. Through the use of country-specific reference values for the index, we demonstrate that it is significantly related to other national phytoplankton assessment systems and illustrate for a single European (intercalibration) lake type how it was used to intercalibrate WFD boundaries from different countries.     

Estimating confidence of European WFD ecological status class and WISER Bioassessment Uncertainty Guidance Software (WISERBUGS)

The Water Framework Directive (WFD) requires estimates of the confidence and precision associated with any scheme for assessing and monitoring the ecological status class of any European rivers, lakes, transitional or coastal waters. This is a complex important issue, especially for waterbody assessments based on multiple metrics and/or two or more taxonomic groups. This paper aims to contribute towards improving understanding and providing practical approaches to assessing confidence of class by (i) discussing the various sources and causes of uncertainty, (ii) using UK rivers macroinvertebrate datasets to illustrate the estimation of replicate, temporal and spatial variance components and the implications for water body metric precision, confidence of class and optimal sampling design, (iii) introducing new freely available general software WISER Bioassessment Uncertainty Guidance Software (WISERBUGS) which uses prior sampling uncertainty estimates with user-specified metrics, class limits and metric combination rules to simulate the joint sampling uncertainty in metric EQR values and provide estimates of confidence of class based on individual metrics, (optionally weighted) multi-metric indices and/or multi-metric classification rules (worst case, mean or median class) based on one or more WFD biological quality elements.     

A comparative review of recovery processes in rivers, lakes, estuarine and coastal waters

The European Water Framework Directive aims to improve ecological status within river basins. This requires knowledge of responses of aquatic assemblages to recovery processes that occur after measures have been taken to reduce major stressors. A systematic literature review comparatively assesses recovery measures across the four major water categories. The main drivers of degradation stem primarily from human population growth and increases in land use and water use changes. These drivers and pressures are the same in all four water categories: rivers, lakes, transitional and coastal waters. Few studies provide evidence of how ecological knowledge might enhance restoration success. Other major bottlenecks are the lack of data, effects mostly occur only in short-term and at local scale, the organism group(s) selected to assess recovery does not always provide the most appropriate response, the time lags of recovery are highly variable, and most restoration projects incorporate restoration of abiotic conditions and do not include abiotic extremes and biological processes. Restoration ecology is just emerging as a field in aquatic ecology and is a site, time and organism group-specific activity. It is therefore difficult to generalise. Despite the many studies only few provide evidence of how ecological knowledge might enhance restoration success.     

M-AMBI derived from taxonomic levels higher than species allows Ecological Status assessments of benthic habitats in new geographical areas

Under the Water Framework Directive (WFD) benthic Ecological Quality Ratios (EQRs) are important tools for assessing Ecological Status (ES) of coastal and transitional waters. Calculation of the Multivariate-AZTI Marine Biotic Index (M-AMBI) EQR is based on the proportions of sensitive and stress tolerant benthic invertebrate species, number of species and Shannon–Wiener diversity. The sensitivity of many tropical/sub-tropical taxa has not yet been determined, presenting a barrier to the direct transfer of WFD EQRs, and the ideas underpinning them, to the management of coastal waters beyond Europe. To overcome this we examine using higher taxonomic level data with M-AMBI.Before applying such approaches to assessing ES in new geographical regions it is essential to determine the effects of using higher taxonomic level data on M-AMBI in areas where the tool was developed. To this end, we use macrofaunal data from three well studied sites in north-western Europe to examine the effects of using taxonomic level data higher than species on M-AMBI. Using the European datasets M-AMBI ES classification was shown to be robust to changes in taxonomic level data. We test the suitability of family-level M-AMBI for assessing ES in subtropical Hong Kong waters. Family level M-AMBI was useful in detecting stress in Hong Kong, where it successfully detected temporal and spatial shifts in ES in response to seasonal hypoxia and salinity variability, and anthropogenic organic enrichment.     

Transitional and coastal waters ecological status assessment: advances and challenges resulting from implementing the European Water Framework Directive

The derivation, performance, sensitivity and inherent uncertainty of ecological quality indicators have become major topics in developing tools for the management of marine, transitional and coastal waters. In reviewing the advances in these waters, related to an ecological status assessment, we show the future challenges to be addressed within the European Water Framework Directive (WFD). Using new analyses carried out under the research project ‘Water Bodies in Europe: Integrative Systems to Assess Ecological status and Recovery’, we provide a complete set of assessments for the biological quality elements (BQEs) (phytoplankton, macroalgae-seagrasses, macroinvertebrates and fish) to be assessed, as well as the validation of existing indicators and multimetric indices and, in some cases, the development of new assessment indices. We show that these indices respond differently to different human pressures and they each have challenges in defining reference conditions against which future changes are judged. In investigating good ecological potential, as the response to heavily modified water bodies, we show that there are flaws in the Directive, not least in its definitions. Our analyses have also focussed on uncertainty in using the indices and we emphasise the problems of defining ecological class boundaries based on indices which themselves may be combined indices (multimetrics). The analysis shows that some of those multimetrics are redundant and/or are inter-correlated and thus may reduce the sensitivity in defining ecological class boundaries. If this is related to the drivers-pressures-state change-impacts-response approach then there are lessons for management measures aimed at achieving good ecological status and even the potential for legal challenges to decisions based on uncertain indices under the WFD. Hence, we conclude the continued need for advances in assessing pressures and gradients, and defining reference conditions for state change, index development, impact assessment and the validation of indices for each BQE.     

River and Riparian Restoration in the Southwest: Results of the National River Restoration Science Synthesis Project

Restoration activity has exponentially increased across the Southwest since 1990. Over 37,000 records were compiled into the National River Restoration Science Synthesis (NRRSS) database to summarize restoration trends and assess project effectiveness. We analyzed data from 576 restoration projects in the Southwest (NRRSS‐SW). More than 50% of projects were less than or equal to 3 km in length. The most common restoration project intent categories were riparian management, water quality management, in‐stream habitat improvement, and flow modification. Common project activities were well matched to goals. Conservative estimates of total restoration costs exceeded $500 million. Most restoration dollars have been allocated to flow modification and water quality management. Monitoring was linked to 28% of projects across the Southwest, as opposed to just 10% nationwide. Mean costs were statistically similar whether or not projects were monitored. Results from 48 telephone interviews provided validation of NRRSS‐SW database analyses but showed that project costs are often underreported within existing datasets. The majority of interviewees considered their projects to be successful, most often based upon observed improvements to biota or positive public reaction rather than evaluation of field data. The efficacy of restoration is difficult to ascertain given the dearth of information contained within most datasets. There is a great need for regional entities that not only track information on project implementation but also maintain and analyze monitoring data associated with restoration. Agencies that fund or regulate restoration should reward projects that emphasize monitoring and evaluation as much as project implementation.     

Application of biotic and taxonomic distinctness indices in assessing the Ecological Quality Status of two coastal lakes: Caprolace and Fogliano lakes (Central Italy)

Marine biotic indices (AMBI, BENTIX) and the statistical tool M-AMBI (Multivariate AMBI) were applied as a comparative approach in assessing the Ecological Quality Status (EcoQS) of two Mediterranean coastal lakes (Caprolace and Fogliano lakes) situated in the Circeo National Park (Central Italy). The macrobenthic community was analysed using univariate indices (community structure), correspondence analysis (CA) and taxonomic distinctness indices (Δ⁺ and Λ⁺). The community composition showed a dominance of lagoonal species in both coastal lakes, while in Caprolace lake marine taxa were also found. Diversity index (H′) complies to ranges found in Mediterranean lagoons and taxonomic distinctness indices demonstrated that taxonomy structure is in accordance with natural variability ranges. Principal component analysis (PCA) on chemical parameters of water and sediment showed that both coastal lakes differ mainly in their organic matter composition. In fact, the protein fraction of bio-polymeric carbon prevails in Fogliano lake, while the ‘refractory’ component represented by carbohydrate fraction is predominant in Caprolace lake. The difference between the two coastal lakes was also demonstrated by co-inertia analysis (COIA) performed using abundance of species and concentrations of chemical parameters. The results from the application of the three biotic indices do not highlight a clear distinction between the two lagoons. However, the AMBI index provided a more suitable evaluation of EcoQS corresponding to ‘slightly polluted’ lagoons while M-AMBI and moreover BENTIX indices indicated a worsening situation. The biotic indices are widely used in assessing the EcoQS in marine environments, but their proper application in transitional waters would depend on a resettlement; thresholds established in the biotic index scale values need to be modified according to natural variability of transitional waters referring to abiotic conditions and abundance of tolerant species.     

Information management at the North Temperate Lakes Long-term Ecological Research site — Successful support of research in a large,diverse, and long running project

Information management has been an integral part of the research process at the North Temperate Lakes Long-term Ecological Research (NTL LTER) program for over 30 years. A combination of factors has made the information management system (IMS) at NTL very successful. Significant resources have been invested in the IMS from the beginning, the Information Manager has been part of the leadership team at NTL and later in various roles at the LTER network level; the NTL IMS was a very early adopter of database systems, standardized metadata, and a data delivery system based on those metadata. This approach has made data easily accessible to NTL researchers and the broader scientific community. Data management workflows have become increasingly more automated with adoption of modern technologies as they became available, making the system efficient enough to handle core data as well as all one-time research data generated within NTL and several related projects. More than three decades of core data from eleven lakes are reused extensively as critical background information and as the limnological go-to site for many synthesis projects within and beyond LTER.The NTL IMS continues to implement new technologies for improving data management efficiency, discovery, access, integration, and synthesis. Accordingly, the functionality of the original online data access system programmed in Java and JavaServer Pages (JSP) was ported to the modern content management system, Drupal and integrated into LTER's Drupal Ecological Information Management System (DEIMS). NTL has invested in sensor technology for studying lake conditions over the long term, which necessitated a sophisticated management system tailored to high frequency data streams. Several technologies have been used at different times for automation of management, quality control and archiving of these high volume data. Near real time lake conditions can be accessed on the NTL website and smart phone Apps.Easy access to long-term and sensor data in the NTL IMS has led NTL researchers to develop new analytical methods and the publication of several R statistical packages. Recent graduate students are now employed as data scientists helping define a new career path inspired by the availability of data.The NTL project has amassed one of the world's most comprehensive long-term datasets on lakes and their surrounding landscapes. The NTL IMS facilitates the use of these data by multiple groups for research, education, and communication of science to the public.     

Site-specific chlorophyll reference conditions for lakes in Northern and Western Europe

The Water Framework Directive (WFD) requires EU Member States to assess the “ecological status” of surface waters. As a component of ecological status, many European countries are developing a classification scheme for chlorophyll concentrations as a measure of phytoplankton biomass. The chlorophyll classification must be based on the degree of divergence of a water body from an appropriate baseline or ‘reference condition’. This article describes the development of a series of regression models for predicting reference chlorophyll concentrations on a site-specific basis. For model development, a large dataset of European lakes considered to be in reference condition, 466 lakes in total, was assembled. Data were included from 12 European countries, but lakes from Northern and Western Europe dominated and made up 92% of all reference lakes. Data have been collated on chlorophyll concentration, altitude, mean depth, alkalinity, humic type, surface area and geographical region. Regression models were developed for estimating site-specific reference chlorophyll concentrations from significant predictor ‘typology’ variables. Reference chlorophyll concentrations were found to vary along a number of environmental gradients. Concentrations increased with colour and alkalinity and decreased with lake depth and altitude. Forward selection was used to identify independent explanatory variables in regression models for predicting site-specific reference chlorophyll concentrations. Depth was selected as an explanatory variable in all models. Alkalinity was included in models for low colour and humic lakes and altitude was included in models for low colour and very humic lakes. Uncertainty in the models was quite high and arises from errors in the data used to develop the models (including natural temporal and spatial variability in data) and also from additional explanatory variables not considered in the models, particularly nutrient concentrations, retention time and grazing. Despite these uncertainties, site-specific reference conditions are still recommended in preference to type-specific reference conditions, as they use the individual characteristics of a site known to influence phytoplankton biomass, rather than adopt standards set to generally represent a large population of lakes of a particular type. For this reason, site-specific reference conditions should result in reduced error in ecological status classifications, particularly for lakes close to typology boundaries.     

IRBAS: An online database to collate,analyze, and synthesize data on the biodiversity and ecology of intermittent rivers worldwide

Key questions dominating contemporary ecological research and management concern interactions between biodiversity, ecosystem processes, and ecosystem services provision in the face of global change. This is particularly salient for freshwater biodiversity and in the context of river drying and flow‐regime change. Rivers that stop flowing and dry, herein intermittent rivers, are globally prevalent and dynamic ecosystems on which the body of research is expanding rapidly, consistent with the era of big data. However, the data encapsulated by this work remain largely fragmented, limiting our ability to answer the key questions beyond a case‐by‐case basis. To this end, the Intermittent River Biodiversity Analysis and Synthesis (IRBAS; http://irbas.cesab.org ) project has collated, analyzed, and synthesized data from across the world on the biodiversity and environmental characteristics of intermittent rivers. The IRBAS database integrates and provides free access to these data, contributing to the growing, and global, knowledge base on these ubiquitous and important river systems, for both theoretical and applied advancement. The IRBAS database currently houses over 2000 data samples collected from six countries across three continents, primarily describing aquatic invertebrate taxa inhabiting intermittent rivers during flowing hydrological phases. As such, there is room to expand the biogeographic and taxonomic coverage, for example, through addition of data collected during nonflowing and dry hydrological phases. We encourage contributions and provide guidance on how to contribute and access data. Ultimately, the IRBAS database serves as a portal, storage, standardization, and discovery tool, enabling collation, synthesis, and analysis of data to elucidate patterns in river biodiversity and guide management. Contribution creates high visibility for datasets, facilitating collaboration. The IRBAS database will grow in content as the study of intermittent rivers continues and data retrieval will allow for networking, meta‐analyses, and testing of generalizations across multiple systems, regions, and taxa.     

A LIMNOLOGICAL SYNOPSIS OF BHANGAZI SOUTH,A DYSTROPHIC COASTAL LAKE IN THE GREATER ST LUCIA WETLAND PARK (KWAZULU/NATAL), WITH COMMENTS ON ITS CONSERVATION VALUE.

Summary

Base-line limnological and biological data are given for Lake Bhangazi South, a small lake on the coastal plain of Kwazulu-Natal, South Africa. This shallow (Z_max < 6 m), subtropical lake is a warm and seemingly continuously polymictic system, but experiences severe (continuous?) deoxygenation of its deeper muddy sediments. Nutrient status (of N in particular), light attenuation, phytoplankton productivity and zooplankton biomass are high relative to other regionally comparable coastal lakes investigated. While the ichthyofauna is quite rich, zooplankton and especially zoobenthos communities are species-poor, and lack the relict estuarine components which often dominate these latter assemblages in comparable coastal lakes. The zooplankton is typically freshwater in composition, and contains a new species of copepod (Tropodiaptomus bhangazii Rayner); the lake may be older, or seen longer evolutionary divergence than its proximate counterparts. Benthic species diversity in the lake is especially low amongst the Crustacea and Mollusca, possibly reflecting the effect of relatively acid waters (pH ca 6.5) on the calcium budgets of these groups. Scanty observational data indicative of ecosystem changes over the past 35 years are reported and briefly evaluated from a conservation/management perspective. Along with the endemic copepod, several rare fish species give the lake added conservation status.     

The AQEM/STAR taxalist – a pan-European macro-invertebrate ecological database and taxa inventory

The European list of aquatic macro-invertebrate taxa, and its associated ecological database, originated within the context of the AQEM project and have been extended during the STAR project. The AQEM/STAR taxalist is a product of co-operation between applied freshwater ecologists and scientists from different zoological fields, applied partners and the administration. The basic idea is that a sound understanding of benthic invertebrate ecology is a prerequisite for the implementation of a biological approach to aquatic ecosystem management in Europe. The database has been generated under the management of BOKU (University of Natural Resources and Applied Life Sciences, Vienna) and UDE (University of Duisburg-Essen) and provides an important means of standardisation and unification of ecological classifications in Europe. This paper outlines the aims for setting up the AQEM/STAR macro-invertebrate taxalist and autecological database and provides a current summary of the numbers of aquatic orders, families, species, and species occurrences in 14 European countries. The number of available and applicable assignments of taxa to each ecological parameter is summarised and examples are given for different parameters and taxonomic groups. Gaps in the autecological information are identified and discussed. Besides its ecological relevance, the operational character of this database is underlined by the fact that it provides the associated taxon codes for each of five different European assessment systems for nearly 10,000 European macro-invertebrate taxa.     

An overview of integrated hydro-ecological studies in the MELMARINA Project: monitoring and modelling coastal lagoons—making management tools for aquatic resources in North Africa

As landscape disturbance and climate conspire to accelerate global environmental change towards unprecedented levels in the twenty-first century, the populated coastal regions of many countries are facing major threats to sustainability. Coastal water resources are particularly vulnerable in dry regions. In view of the expected severity of future environmental change in the Southern Mediterranean Region, the European Commission supported an integrated multidisciplinary project, MELMARINA, on monitoring and modelling coastal lagoons in Morocco, Tunisia and Egypt. This is a region where water management for people and for agriculture has been intense particularly during the twentieth century, yet long-term environmental monitoring and management of wetland ecosystems are under developed. Not only are biodiversity aspects at risk in coastal lagoons and wetlands but the goods and services that affect human welfare are also generally in decline. Co-ordinated hydro-ecological monitoring at key wetland lagoons was begun in 2003 with a view to establishing environmental baselines and calibrating site-specified hydro-ecological models. This article introduces the project and its results that range from lagoon typification and hydro-ecology to the application of hydro-ecological models. Detailed results and evaluations are presented in a linked series of themed scientific articles within this special issue. The present condition of the lagoons investigated essentially results from various hydrological modifications combined with eutrophication problems, yet all still remain valuable aquatic ecosystems. Adequate monitoring data are an essential part of reliable predictive modelling and, despite several data gaps, nutrient load reduction scenarios were undertaken to help target restoration aims. Implementation of aspects of the EU Water Framework Directive for achieving good ecological status of transitional waters is advocated. Nevertheless, as the twenty-first century advances the effects of global climate change are expected to amplify current stresses making intervention restoration and adaptation management even more imperative. Long-term sustainability depends upon detecting and measuring environmental change (long-term water quality and ecological quality) and incorporating the results into appropriate hydro-ecological models to facilitate the development of appropriate management initiatives. Guest editors: J. R. Thompson & R. J. Flower Hydro-ecological Monitoring and Modelling of North African Coastal Lagoons     

Acid rain — perspectives on lake recovery

During the 1970‘s and 1980‘s, the acidification of surface waters by atmospherically deposited sulphur became a major international concern. Large sulphur emission control programs were implemented in Europe and North America with the expectation that many affected aquatic ecosystems would recover. Because of a variety of factors, these positive expectations have been slow to be realized. Only limited evidence of the chemical recovery of acid lakes has emerged from areas other than the Sudbury, Canada region, where sulphur emission reductions were particularly large. Lake response models indicate that when current sulphur emission control strategies in Europe and North America are fully implemented, many lakes will still be acid-damaged even though substantial overall improvements in lake chemistry are expected. An increasing body of evidence indicates that substantial biological recovery, among many groups of organisms,can be expected when chemical conditions improve in lakes. Not all species, however, are capable of unassisted recovery and some lakes can pose biological or physical barriers to colonizers. Thus, stocking may be an important element in management strategies for the restoration of some recovering lakes. Communities in recovered lakes may not achieve pre disturbance conditions, but establishment of typical communities appears to be a reasonable recovery target. This revised version was published online in July 2006 with corrections to the Cover Date.     

Simple tools for assessing water quality and trophic status in transitional water ecosystems

In this study we have developed an index for assessing trophic status and water quality in transitional aquatic ecosystems of Southern Europe. The index has been developed from the water quality index of the U.S. National Sanitation Foundation and integrates the main causal factors (inorganic nutrients), the key biological elements (primary producers) and indicator of effects (oxygen) of eutrophication. Six main variables have been used: relative coverage of benthic phanerogams and opportunistic macroalgae species, and concentrations of dissolved oxygen, phytoplankton chlorophyll-a, dissolved inorganic nitrogen and phosphorus. Non-linear functions are used to transform each measured variable into its quality value. Each quality value is then multiplied by a weighting factor, to take into account the relative contribution of each variable to the overall water quality. Finally, the index value is calculated as the sum of the weighted quality values, ranging from 0 (poorest state) to 100 (best condition). The index has been tested and validated in six transitional water ecosystems which differ in anthropogenic pressures and eutrophication levels, for which data sets were available from 1989 to 2004: Sacca di Goro (Northern Adriatic Sea, Italy), Lesina Lagoon (Southern Adriatic Sea, Italy), Ria Formosa (Algarve, Southern Portugal), Mar Menor (Murcia, Southern Spain), Etang de Thau (Herault, Southern France) and Gulf of Gera (Lesvos Island, Greece). The index assessments have been compared with evaluations from the IFREMER (French Research Institute for the Exploitation of the Sea) classification scheme (France) and the trophic index TRIX (Italy), which are currently used for national monitoring of coastal waters and lagoons. Based on the conclusions of this study we suggest to use the index for monitoring water quality in shallow coastal transitional waters, where benthic vegetation controls primary productivity, which makes indices based on phytoplankton only (e.g., TRIX) unsuitable.