This opinion paper introduces a special series of articles dedicated to freshwater benthic algae and their use in assessment and monitoring. This special series was inspired by talks presented at the 9th International Congress on the Use of Algae for Monitoring Rivers and Comparable Habitats (Trento, Italy, 2015), the latest of a series of meetings started in 1991. In this paper, we will first provide a brief overview of phytobenthos methods in Europe. Then, we will turn towards the 'dark side' of phytobenthos and describe four particular problems for phytobenthos assessment in the European Union: (1) over-reliance on a single group of algae (mostly diatoms) to the exclusion of other groups; (2) relatively low adoption of benthic algae for ecological assessments in lakes; (3) absence of measures of phytobenthos abundance; (4) approaches used to define boundaries between ecological classes. Following this, we evaluate the strengths and limitations of current phytobenthos assessment methods against 12 criteria for method evaluation addressing four areas: ecological rationale, performance, feasibility of implementation, and use in communication and management. Using these criteria, we identify and discuss three general challenges for those developing new methods for phytobenthos-based assessment: a weak ecological rationale and insufficient consideration of the role of phytobenthos as a diagnostic tool and for communicating ecosystem health beyond a narrow group of specialists. The papers in the special series allow a comparison with the situation and approaches in the USA, present new methods for the assessment of ecological status and acidification, provide tools for an improved management of headwaters and petrifying springs, discuss the utility of phytobenthos for lake assessments, and test the utility of functional measures (such as biofilm phosphorus uptake capacity, PUC).

Legislation in Europe has been adopted to determine and improve the ecological integrity of inland and coastal waters. Assessment is based on four biotic groups, including benthic macroinvertebrate communities. For lakes, benthic invertebrates have been recognized as one of the most difficult organism groups to use in ecological assessment, and hitherto their use in ecological assessment has been limited. In this study, we review and intercalibrate 13 benthic invertebrate-based tools across Europe. These assessment tools address different human impacts: acidification (3 methods), eutrophication (3 methods), morphological alterations (2 methods), and a combination of the last two (5 methods). For intercalibration, the methods were grouped into four intercalibration groups, according to the habitat sampled and putative pressure. Boundaries of the 'good ecological status' were compared and harmonized using direct or indirect comparison approaches. To enable indirect comparison of the methods, three common pressure indices and two common biological multimetric indices were developed for larger geographical areas. Additionally, we identified the best-performing methods based on their responsiveness to different human impacts. Based on these experiences, we provide practical recommendations for the development and harmonization of benthic invertebrate assessment methods in lakes and similar habitats.

The concept of “reference conditions” describes the benchmark against which current conditions are compared when assessing the status of water bodies. In this paper we focus on the establishment of reference conditions for European lakes according to a phytoplankton biomass indicator—the concentration of chlorophyll-a. A mostly spatial approach (selection of existing lakes with no or minor human impact) was used to set the reference conditions for chlorophyll-a values, supplemented by historical data, paleolimnological investigations and modelling. The work resulted in definition of reference conditions and the boundary between “high” and “good” status for 15 main lake types and five ecoregions of Europe: Alpine, Atlantic, Central/Baltic, Mediterranean, and Northern. Additionally, empirical models were developed for estimating site-specific reference chlorophyll-a concentrations from a set of potential predictor variables. The results were recently formulated into the EU legislation, marking the first attempt in international water policy to move from chemical quality standards to ecological quality targets.

Summary: The implementation of the Water Framework Directive requires EU member states to establish and harmonize ecological status class boundaries for biological quality elements. In this paper, we describe an approach for defining ecological class boundaries that delineates shifts in lake ecosystem functioning and, therefore, provides ecologically meaningful targets for water policy in Europe. We collected an extensive data set of 810 lake‐years from nine Central European countries, and we used phytoplankton chlorophyll a, a metric widely used to measure the impact of eutrophication in lakes. Our approach establishes chlorophyll a target values in relation to three significant ecological effects of eutrophication: the decline of aquatic macrophytes, the dominance of potentially harmful cyanobacteria and the major functional switch from a clear water to a turbid state. Ranges of threshold chlorophyll a concentrations are given for the two most common lake types in lowland Central Europe: for moderately deep lakes (mean depth 3–15 m), the greatest ecological shifts occur in the range 10–12 μg L⁻¹ chlorophyll a, and for shallow lakes (<3 m mean depth), in the range 21–23 μg L⁻¹ chlorophyll a. Synthesis and applications. Our study provides class boundaries for determining the ecological status of lakes, which have robust ecological consequences for lake functioning and which, therefore, provide strong and objective targets for sustainable water management in Europe. The results have been endorsed by all participant member states and adopted in the European Commission legislation, marking the first attempt in international water policy to move from physico‐chemical quality standards to harmonized ecologically based quality targets.

Lakes in Europe are subject to multiple anthropogenic pressures, such as eutrophication, habitat degradation and introduction of alien species, which are frequently inter-related. Therefore, effective assessment methods addressing multiple pressures are needed. In addition, these systems have to be harmonised (i.e. intercalibrated) to achieve common management objectives across Europe. Assessments of fish communities inform environmental policies on ecological conditions integrating the impacts of multiple pressures. However, the challenge is to ensure consistency in ecological assessments through time, across ecosystem types and across jurisdictional boundaries. To overcome the serious comparability issues between national assessment systems in Europe, a total anthropogenic pressure intensity (TAPI) index was developed as a weighted combination of the most common pressures in European lakes that is validated against 10 national fish-based water quality assessment systems using data from 556 lakes. Multi-pressure indices showed significantly higher correlations with fish indices than single-pressure indices. The best-performing index combines eutrophication, hydromorphological alterations and human use intensity of lakes. For specific lake types also biological pressures may constitute an important additional pressure. The best-performing index showed a strong correlation with eight national fish-based assessment systems. This index can be used in lake management for assessing total anthropogenic pressure on lake ecosystems and creates a benchmark for comparison of fish assessments independent of fish community composition, size structure and fishing-gear. We argue that fish-based multiple-pressure assessment tools should be seen as complementary to single-pressure tools offering the major advantage of integrating direct and indirect effects of multiple pressures over large scales of space and time.

Although the Water Framework Directive specifies that macrophytes and phytobenthos should be used for the ecological assessment of lakes and rivers, practice varies widely throughout the EU. Most countries have separate methods for macrophytes and phytobenthos in rivers; however, the situation is very different for lakes. Here, 16 countries do not have dedicated phytobenthos methods, some include filamentous algae within macrophyte survey methods whilst others use diatoms as proxies for phytobenthos. The most widely-cited justification for not having a dedicated phytobenthos method is redundancy, i.e. that macrophyte and phytoplankton assessments alone are sufficient to detect nutrient impacts. Evidence from those European Union Member States that have dedicated phytobenthos methods supports this for high level overviews of lake condition and classification; however, there are a number of situations where phytobenthos may contribute valuable information for the management of lakes.