An approach to intercalibrate ecological classification tools using fish in transitional water of the North East Atlantic

A simple procedure to harmonise and intercalibrate eight national methods classifying the ecological status using fish in transitional waters of the North East Atlantic is described. These methods were initially intercalibrated and a new method recently developed was added to this exercise. A common human pressure index pre-classified the status of each water body in an independent way. Ecological class boundaries values were established according to the level of anthropogenic pressure using regression analyses. A simulated dataset was used to assess the level of agreement between the fish classification methods. Fleiss’ multi-rater kappa analysis indicated that boundary harmonisation was achieved; all classifications fell within one class of each other and class agreement between methods exceeded 70%. The use of a pressure index to establish boundary thresholds provides a practical method of defining and harmonizing the quality classes associated with human pressures, as required by the European Water Framework Directive.     

Integration of the saprobic system into the European Union Water Framework Directive – Case studies in Austria,Germany and Czech Republic

The use of saprobic systems has long traditions in the water management in Austria, the Czech Republic and Germany. Within the context of water quality assessment they are applied to indicate the effects of anthropogenic caused organic impact leading to a decrease in the dissolved oxygen content of running waters. In December 2000 the European Union Water Framework Directive (WFD) came into force. It demands homogeneous procedures and methods for assessing inland surface waters as well as groundwater, coastal and transitional waters. The WFD focuses on the assessment of biotic elements and the ecological status has to be defined based on type specific approaches and reference conditions. To incorporate the saprobic approach into the new integrative methodology of the European assessment of the ecological status of water bodies, the national saprobic systems need to be adjusted. This paper describes the according methodological developments and adaptations of Austria, the Czech Republic, and Germany required to harmonise the traditional procedure with the guidelines of the WFD. In the three countries national databases were established to provide species lists from largely undisturbed stream sites. Such reference sites build the basis for calculating stream type specific reference values. The calculation has been done in slightly different ways dependent on the country. In addition to that boundaries were defined to characterise the 5 saprobic quality classes.     

Phytoplankton communities and biomass size structure (fractionated chlorophyll “a”), along trophic gradients of the Basque coast (northern Spain)

Eutrophication is a major threat to coastal ecosystems. Within Europe, the Water Framework Directive (WFD) has established the need of developing methods of assessment. Bulk chlorophyll “a” is used world-wide as an indicator of eutrophication. However, the size structure of the phytoplankton communities has not been investigated, in detail, in relation to eutrophication pressures. This study investigates the suitability of fractionated chlorophyll “a” (<10 and >10 μm), as an indicator of eutrophication. Along the Basque coast (northern Spain) several water bodies, ranging from offshore waters to the heads of the estuaries, were surveyed during 2008. Physico-chemical conditions and chlorophyll “a” showed a distinct spatial gradient. Trophic richness increased towards the middle and inner parts of the estuaries, where nutrient inputs, from natural or anthropogenic sources, together with the residence time of the water are usually higher. In summer, phytoplankton biomass and abundance decreased, generally, in offshore and coastal waters; in estuaries, they tended to increase. The chlorophyll distribution within the two size fractions was coherent with the phytoplankton taxonomic composition. In summer, the relative abundance of small-sized cells (diatoms and non-siliceous taxa) increased. The relationships between size-fractionated chlorophyll and physico-chemical variables differed, when comparing the offshore and coastal waters, with the estuaries. In the offshore and coastal waters, a strong seasonality was observed; in estuaries, an important spatial component was found. Fractionated chlorophyll provided complementary useful information on anthropogenic pressures. However, more research is necessary to utilise this variable as a tool for ecological status assessment, within the WFD.     

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.     

Application of a new multi-metric phytoplankton index to the assessment of ecological status in marine and transitional waters

Patterns of phytoplankton size spectra variation with gradients of environmental stress have been observed in freshwater, transitional waters and marine ecosystems, driving the development of size spectra based assessment tools.In this study, we have tested on transitional and coastal waters a new Index of Size spectra Sensitivity of Phytoplankton (ISS-Phyto), which integrates simple size spectra metrics, size class sensitivity to anthropogenic disturbance, phytoplankton biomass (chlorophyll a) and taxonomic richness thresholds. ISS-Phyto has been tested both among and within ecosystems along pressure gradients based on expert view assessment; the adequacy of symmetric and both left and right asymmetric models of phytoplankton size class sensitivity have been compared.The results showed that ISS-Phyto consistently discriminated between anthropogenic and natural disturbance conditions. Left asymmetric models of size spectra sensitivity, assuming greater disturbance tolerance with respect to eutrophication and organic enrichment of increasingly large size classes, showed the best fit comparing all ecosystems; in three of the four considered ecosystems (Varna, Helsinki, Mompás-Pasaia), they seemed to discriminate best between different levels of disturbance also within ecosystems. Moreover, they demonstrated significant and inverse patterns of variation along the overall pressure gradient as well as along the inorganic phosphorus (DIP), chlorophyll a and trophic index (TRIX) gradients.Therefore, ISS-Phyto, originally developed for transitional waters, seems to be an adequate assessment tool of ecological status also in coastal marine waters; moreover, it seems adequate to describe within ecosystem disturbance gradients. Hence, ISS-Phyto helps to understand the relationships between anthropogenic impact and ecosystem response from the individual point of view, with reference to the simple parameter of body size.     

Decoding Size Distribution Patterns in Marine and Transitional Water Phytoplankton: From Community to Species Level

Understanding the mechanisms of phytoplankton community assembly is a fundamental issue of aquatic ecology. Here, we use field data from transitional (e.g. coastal lagoons) and coastal water environments to decode patterns of phytoplankton size distribution into organization and adaptive mechanisms. Transitional waters are characterized by higher resource availability and shallower well-mixed water column than coastal marine environments. Differences in physico-chemical regime between the two environments have been hypothesized to exert contrasting selective pressures on phytoplankton cell morphology (size and shape). We tested the hypothesis focusing on resource availability (nutrients and light) and mixed layer depth as ecological axes that define ecological niches of phytoplankton. We report fundamental differences in size distributions of marine and freshwater diatoms, with transitional water phytoplankton significantly smaller and with higher surface to volume ratio than marine species. Here, we hypothesize that mixing condition affecting size-dependent sinking may drive phytoplankton size and shape distributions. The interplay between shallow mixed layer depth and frequent and complete mixing of transitional waters may likely increase the competitive advantage of small phytoplankton limiting large cell fitness. The nutrient regime appears to explain the size distribution within both marine and transitional water environments, while it seem does not explain the pattern observed across the two environments. In addition, difference in light availability across the two environments appear do not explain the occurrence of asymmetric size distribution at each hierarchical level. We hypothesize that such competitive equilibria and adaptive strategies in resource exploitation may drive by organism’s behavior which exploring patch resources in transitional and marine phytoplankton communities.     

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.     

Comparison of two indices based on macrophyte assemblages to assess the ecological status of coastal waters in the transition between the Atlantic and Mediterranean eco-regions

Several indices based on the composition and abundance of aquatic flora have been developed to assess the ecological status of coastal waters along the European coasts in the context of the Water Framework Directive. This directive pointed out the intercalibration of indices based on the same biological element within an eco-region to ensure the consistency and comparability among them. For a better management of coastal areas in the transition zone between two eco-regions, the comparison of indices developed for each eco-region may also be necessary. The aim of this work was to compare two indices based on macrophytes that have been proposed for two different and adjoining eco-regions: the RSL (Reduced Species List) in the Atlantic eco-region and the CARLIT (Cartography of littoral and upper sublittoral communities) in the Mediterranean. These indices were applied in 14 sites in the transition between the Atlantic Ocean and the Mediterranean Sea, where a wide range of anthropogenic pressures can be found, from high (Algeciras Bay) to almost negligible ("El Estrecho" Natural Park). Overall, both indices were sensitive to anthropogenic pressures and suitable to assess the ecological status. The comparison between indices suggested a bias in the assessment of the ecological status between good and high classes due to a different definition of high ecological status class between RSL and CARLIT. In addition, the most important disagreements between indices were found in the most degraded localities. The results showed, however, a high comparability between RSL and CARLIT despite their marked conceptual and methodological differences.     

Ecological assessment of soft bottom benthic communities in northern Spanish estuaries

The implementation of the Water Framework Directive requires the classification of the ecological quality status of benthic macroinvertebrates in costal and transitional waters. The uncertainty and complexity of this task have lead to the creation of specific Geographical Intercalibration Groups (GIGs) for the different ecoregions and types of water bodies established. In this framework, several metrics are under study in the United Kingdom, Spain and Denmark for North East Atlantic coastal waters (NEA-GIG). All of them include in their formulations the AMBI index. Nevertheless, few advances have been made in relation to transitional waters. This paper aims to test the suitability of those methodological procedures for their application in Northern Spanish estuaries. The results show evident divergences in classification of ecological status among methods, although the correlations of corresponding ecological quality ratios (EQRs) are good. Thus, we think that it may be necessary to modify the boundaries between each ecological status category and adjust the reference conditions for the variety of community-types existing in estuarine water bodies. However, some problems arise in the assessment of some naturally stressed communities. In this situation, we found an overall dominance of species tolerant to organic enrichment in all status categories and low range of variation of AMBI index. This aspect introduces some uncertainty in relation to the ability of this index to detect a deleterious effect in these estuarine communities naturally stressed. On the other hand, we found some sites that achieve good status according to the metrics used, even though the number of opportunistic species was high. The use of combined approaches that incorporate physicochemical condition of sediments would be a straightforward approach to reduce the risk of failing in the assignation of ecological status category.     

An angiosperm quality index (AQI) for Cantabrian estuaries

Angiosperms are an important biological parameter for establishing the status in transitional waters. Angiosperms grow from subtidal to upper intertidal zones and are sensitive to the most important pressures present in estuaries. A multi-metric for determining the status of Cantabrian estuaries has been developed by taking into account the angiosperms that live in these environments. This metric integrates two important directives: the Water Framework Directive (WFD) and the Habitats Directive. To be precise, the diversity of the existing habitats, the coverage in relative terms with respect to the optimal situation, and the loss of extension are considered in the metric. The application of the method to three Cantabrian estuaries subjected to different pressures demonstrates that the metric captures the degree of pressures of each estuary. The multi-metric method allows us to identify the type of problems to be tackled by the relevant authorities in the programme of measures of the river basin management plan.     

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.     

Ability of phytoplankton trait sensitivity to highlight anthropogenic pressures in Mediterranean lagoons: A size spectra sensitivity index (ISS-phyto)

Size spectra exhibit common patterns of variation and predictable responses to pressures across ecosystem types, functional guilds and taxonomic groups. Here, we extend the size spectra approach to phytoplankton ecological status assessment in transitional waters by developing, testing and validating a multi-metric index of size spectra sensitivity (ISS-phyto), which integrates size structure metrics with others such as phytoplankton diversity, biomass and sensitivity of size classes to anthropogenic disturbance. The ability of various theoretical models of size spectra sensitivity to discriminate between disturbed and undisturbed ecosystems and levels of anthropogenic stress was evaluated. We used data on phytoplankton samples collected in 14 Mediterranean and Black sea transitional water ecosystems (coastal lagoons) from Italy, Albania, Greece, Bulgaria and Romania, and compared the models’ efficiency by looking at their pressure–impact response along salinity and enrichment gradients, the latter quantified as variations in dissolved inorganic nitrogen (DIN) and dissolved inorganic phosphorus (DIP). Data from a fifteenth Mediterranean lagoon was used for external validation purposes. Right asymmetric models of size class sensitivity, implying higher sensitivity of smaller cell size classes, were found to contribute to the ISS-phyto multimetric tool more effectively than symmetric and left asymmetric models, distinguishing disturbed from undisturbed lagoons and disturbed from undisturbed stations within the same lagoon. When based on right asymmetric sensitivity models, i.e., those that were most efficient in identifying anthropogenic impacts, ISS-phyto also showed the best fit of pressure–response relationships along the salinity and enrichment gradients; at low to high levels of impact ISS response was driven by size class sensitivity and at very high impacts by phytoplankton biomass. A scheme for the classification of Ecological Quality Status based on ISS-phyto is proposed and validated. The validation procedure found that ISS-phyto is an effective and sensitive monitoring tool, robust, easy to apply and to inter-calibrate among laboratories.     

Development of an Angiosperm Quality Assessment Index (AQuA-Index) for ecological quality evaluation of Portuguese water bodies—A multi-metric approach

Salt marsh vegetation is one important biological element for establishing the ecological quality status (EQS) while evaluating transitional waters (TW). This intertidal plant community is sensitive to the most important pressures present in estuaries. In this study, an ecological index based multi-metric was established taking into account the species composition and ecological relations in Portuguese salt marsh habitats. During the AQuA-Index elaboration it was found that the parameters that respond better to the variability of ecological conditions present nowadays are the Shannon Diversity Index, the Shannon Maximum Diversity Index, the number of halophytic species, the Margalef Diversity Index and the Pielou Equitability Index. The application of the AQuA-Index index to eight TW systems varying in morphology and pressures, demonstrated that the metric responds to the ecological quality of each system. Also, it showed some advantages in comparison with other approaches, in zones with a relevant proportion of middle and upper marsh and where historical data were not available. This way the AQuA-Index proved to be an efficient Index for ecological quality assessment, using salt marsh vegetation as indicator.     

Pollution in Peter the Great Bay, Sea of Japan, and its biological consequences

This review summarizes information published in the 1980s–1990s about anthropogenic pollution in Peter the Great Bay, the largest of the bays in the northwestern part of the Sea of Japan. The coastal zone of the bay occupies about 12% of the area of Primorskii Province and is the most heavily populated. The bulk of the human settlements, the seaports of Vladivostok and Nakhodka, railways, industrial enterprises, and developed agriculture are located in the coastal zone. Sewage waters containing multicomponent mixtures of polluting agents of both mineral and organic origin are discharged into the coastal waters of the bay. This paper presents information about the concentration of major classes of polluting agents (oil hydrocarbons, polychlorinated hydrocarbons, surfactants, heavy metals, and radionuclids) in the water and bottom sediments of the bay. The results of physico-chemical and biogeochemical investigations performed in the 1970s–1990s justify considering Zolotoi Rog Bay, Bosfor Vostochnyi Strait, Nakhodka Bay (especially its innermost portion, around the harbor of Nakhodka), and Amurskii Bay to be the most polluted areas in Peter the Great Bay. The information about the biological consequences of pollution in these water areas is briefly reviewed.     

Larval fish body growth responses to simultaneous browning and warming

Organisms are facing global climate change and other anthropogenic pressures, but most research on responses to such changes only considers effects of single drivers. Observational studies and physiological experiments suggest temperature increases will lead to faster growth of small fish. Whether this effect of warming holds in more natural food web settings with concurrent changes in other drivers, such as darkening water color (“browning”) is, however, unknown. Here, we set up a pelagic mesocosm experiment with large bags in the Baltic Sea archipelago, inoculated with larval Eurasian perch (Perca fluviatilis) and zooplankton prey and varying in temperature and color, to answer the question how simultaneous warming and browning of coastal food webs impact body growth and survival of larval perch. We found that browning decreased body growth and survival of larval perch, whereas warming increased body growth but had no effect on survival. Based on daily fish body growth estimates based on otolith microstructure analysis, and size composition and abundance of available prey, we explain how these results may come about through a combination of physiological responses to warming and lower foraging efficiency in brown waters. We conclude that larval fish responses to climate change thus may depend on the relative rate and extent of both warming and browning, as they may even cancel each other out.     

The CARLIT method for the assessment of the ecological quality of European Mediterranean waters: Relevance,robustness and possible improvements

The application of the European Union (EU) Water Framework Directive (WFD) requires the assessment of the ecological status (ES) of coastal waters in order to detect environmental changes and implement management plans to prevent their further deterioration. The ES of a water body (WB) has to be assessed on the basis of the status of several biological indicators, referred to as biological quality elements (BQE), such as phytoplankton, macroalgae, seagrasses, macroinvertebrates and fish. We present the most extensive assessment ever undertaken of the ES of Mediterranean waters, by means of the CARLIT index, the most widely used index for the Mediterranean Sea. This index is based on the Ecological Quality Ratio (EQR) between a measured value of Ecological Quality (EQ) and a value corresponding to a reference site. This assessment is based on an extensive field study, covering the whole of the Mediterranean French coasts (including Corsica), 40 WBs and ∼2 970 kilometres of shore (at a 1/2 500 scale). The original Ballesteros CARLIT method is compared to the Nikolić modified method, and we have undertaken the challenge of developing an alternative new simplified CARLIT method. This simplified method, which requires less expert judgement, is easier to implement by local authorities, and provides results similar overall to those of the original method. Previous attempts, if any, to correlate EQRs with anthropogenic stressors (through pressure indices) were mainly based upon land uses or on comprehensive lists of stressors, some spatially very sporadic, temporally highly variable, non-representative of the WB and with the impact poorly established on species and communities. To date, the LUSI (Land Uses Simplified Index) and the MA-LUSI-WB have been the most widely used pressure indices. Here, we propose a new pressure index (HAPI) taking into consideration the possible shortcomings of previous indices. It takes into account the actual pressures at community levels considered by the CARLIT method. It accounts well for the EQR values of the study area, as evidenced by the high correlation coefficient between EQRs and HAPI, better than that of the other pressure indices. The present study provides a comprehensive view of the ES of the French Mediterranean coasts. Surprisingly, the picture is far less cause for concern than expected, although this could result from an artefact due to the focus on superficial waters and habitats inherent to the CARLIT method. Where two successive assessments were performed (23 WBs, 2007–2010 vs 2012–2015), the results were similar, which stresses the robustness of the method and/or the relative stability over time of the overall ES of the WBs, and suggests that the successive assessments could be carried out at low frequency.     

Complex patterns in phytoplankton and microeukaryote diversity along the estuarine continuum

Estuaries and coastal lagoons are included within the transitional waters category, according to the Water Framework Directive. However, criteria for their differentiation and characterisation are still under discussion and require more research. In particular, detailed observations of biodiversity in more complex transitional and coastal waters are lacking. Microscopic and molecular analyses were therefore used to investigate phytoplankton diversity and spatial community structure, in early spring, along the freshwater-to-marine continuum of the Segura River (Spain), an intensively regulated semiarid basin discharging into the Mediterranean Sea. In addition to the salinity gradient as the major factor determining taxa distribution, influence of multiple anthropogenic and climatic impacting factors (drought, confined waters, irrigation canal) leads to a significant spatial heterogeneity of the aquatic habitat types associated with variations in community composition. Several shifts within the phytoplankton distribution pattern along the continuum are revealed using multivariate analyses. An impressive bloom of the cryptophyte Plagioselmis prolonga occurred in the mixing zone, associated with a typical euryhaline community indicative of eutrophication. The 18S rDNA diversity revealed a microeukaryotic richness including several little-known groups, heterotrophic representatives, and potential parasites. By combining morphological and molecular approaches we revealed the presence of a ‘hidden’ diversity often neglected in traditional surveys.     

A benthic perspective in assessing the ecological status of estuaries: The case of the Mondego estuary (Portugal)

In transitional waters the process of defining reference conditions (in the scope of the WFD) must account for the natural great variability of such environments. Therefore, stretches reflecting different physical–chemical and biological conditions throughout the system should be defined in order to correctly establish benthic specific reference conditions. Both salinity and sediment structure are major factors controlling physical–chemical conditions and therefore organisms’ distribution within an estuary. These environmental variables (salinity, sediment grain size composition and organic matter content) patterns were studied in the Mondego estuary and some clear gradients emerged. Also, ecological indices (AMBI, Margalef and Shannon-Wiener) were applied to subtidal benthic communities of the Mondego estuary and, generally, there was not only evidence of a decrease in diversity in the estuary from the downstream section towards its inner parts, but also differences were found between areas of distinct sediment composition. After comparing environmental patterns with biodiversity trends, the information was used to define homogeneous sectors along a temperate estuary in Portugal. In the Mondego estuary six zones, covering the main physical gradients affecting benthic communities, were defined: four in the northern arm and two in southern arm. Zones established will allow future determination of benthic reference conditions adjusted for each of the sectors, according to their characteristics, and consequently the conditions they provide for benthic assemblages settlement.     

Benthic macrophyte metrics as bioindicators of water quality: towards overcoming typological boundaries and methodological tradition in Mediterranean and Black Seas

Benthic macrophyte communities of different substratum types (soft, hard) were studied in eleven differently impacted sites belonging in two different water typologies (transitional waters: Lesina Lagoon, Varna Lake; coastal waters: Varna Bay) and two ecoregions (Mediterranean Sea, Black Sea). Species lists were compiled for each study site, 20 taxa were found at Lesina and Varna Lake and Bay, and the abundance of each taxon was determined at each site. The relationship between nine metrics related to community structure [species richness, % of total coverage, dry biomass (g/m^?2), and cluster and multi-dimensional scaling plot of Bray–Curtis similarity] and function [Ecological Status Group I % coverage, ESG II % coverage, Ecological Evaluation Index (EEI-c) and Ecological Index (EI_EEI)] and key abiotic factors and an anthropogenic stress index (EnII) were studied. A strong relationship (Spearman rank correlation coefficient ρ ≤ ?0.89; R ² ≥ 0.89) between anthropogenic stress and functional indices, EEI-c and EI_EEI, was found. The structural index ‘species richness’ correlated negatively with EnII and positively with salinity, demonstrating a freshwater and confinement influence on species diversity. EEI-c and EI_EEI indices classified the studied sites and locations in different Ecological Status Classes in accordance with the anthropogenic stress gradient.