Appendix 1. Water Framework Directive

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The Water Framework Directive (WFD) is the most substantial piece of water legislation ever produced by the European Commission, and provides the major driver for achieving sustainable management of water in the UK and other EU Member States for many years to come.

It requires that all inland and coastal waters bodies within defined river basin districts must reach at least "Good Ecological Status (GES)" by 2015 and defines how this should be achieved through the establishment of environmental objectives and ecological targets for surface waters. For water bodies that have been designated as Heavily Modified (HMWB) or Artificial, they must reach at least "Good Ecological potential (GEP)", and that „ no deterioration‟ should occur in any water body.

In summary, the Directive requires that all surface waters and groundwaters within defined river basin districts must reach at least "good" status by 2015. It will do this for each river basin district by;

  • Defining what is meant by "good" status by setting environmental quality objectives for surface waters and groundwaters;
  • Identifying in detail the characteristics of the river basin district, including the environmental impact of human activity;
  • Assessing the present water quality in the river basin district;
  • Undertaking an analysis of the significant water quality management issues;
  • Identifying the pollution control measures required to achieve the environmental objectives;
  • Consulting with interested parties about the pollution control measures, the costs involved and the benefits arising.

1. WFD Monitoring

Implementing the agreed control measures, monitoring the improvements in water quality and reviewing progress and revising water management plans to achieve the quality objectives.

The WFD requires that an integrated monitoring program be established within each river basin districts. These monitoring programs will in many cases be extensions of modifications of existing monitoring programs and will collect and collate chemical, physical and biological data necessary to assess the status of surface water and groundwater bodies in each river basin district.

There are three types of monitoring under the WFD, these are:

  • Surveillance monitoring which will be used to validate risk assessments and determine long-term changes.
  • Operational monitoring, to determine the status of water bodies identified as being at risk and how this changes as result of the programme of measures.
  • Investigative monitoring, which will be used to establish reasons for failure.

It is envisaged that the river restoration monitoring may well differ from the standard WFD monitoring but may fall under the WFD investigative monitoring category. However, river restoration monitoring may be totally independent of the WFD, though many of its outputs may still be utilised in assessing river basin catchments if only with respect to gaining more knowledge about the catchment and how it operates.

The main reasons for undertaking monitoring for the WFD are to:

  • Establish an overview of the water status of each river basin district
  • Classify individual water bodies as to their water status

For each surface waterbody, the Competent Authorities will assess as appropriate:

  • Biology (plankton/phytobenthos, macrophytes, invertebrates and fish);
  • Hydromorphology;
  • Physico-chemical (including organic pollutants);
  • Priority and priority-hazardous substances.

For groundwaters the monitoring requirements cover:

  • Groundwater resources through a water level monitoring network;
  • Surveillance and operational monitoring of chemical status (Common Implementation Strategy, 2003a)

For more information see :

2. Determining which pressure is causing biological failure

Figure A1.1 An overview of the current practice used to determine which pressure is causing a biological failure

The following information was circulated to members of the Defra Water Stakeholders Forum in October 2011, and gives an overview of how staff in the Environment Agency determine which pressures cause biological failure. While their ecologists use standard methods and data tools, the interpretation of ecological data is an exploratory process. The procedure described below is not prescriptive but is an overview of current practice.

Environment Agency Practice

The following text is written with reference to Figure A1.1 which gives an overview of the current practice used to determine which pressure is causing a biological failure.

When considering the causes of biological failure at a water body (Box 1), we generally take four things into account:

  • Our professional knowledge of the response of biology to pressures
  • The existing pressures in the water body and wider catchment taking local knowledge into account
  • The tools and methods that we use to diagnose the causes of biological pressure (examples in Appendix 1)
  • Existing biological data (including external data), its trends and its statistical associations with pressures

Taking these into account we may be able to infer the causes of the failure, or not (Box 2).

If we can infer the likely cause, then we assess if the level of evidence linking the pressure with the biological failure is sufficient to support action (Box 3) as set out in the guidance on 'Levels of evidence for completing investigations and selecting measures'. Where there is sufficient evidence, the next steps, for example an investigation to determine the source of the pressure and/or implementing measures, can proceed. However, if the level of evidence does not support action, i.e. there is insufficient evidence linking the pressure to the biological impact to justify action, then we conclude that we can‟t infer the cause of the failure with sufficient confidence (Box 6).

If we can't infer the likely cause of failure based on the initial assessment (Box 2), then we need to judge if the current data is adequate for the application of the diagnostic tools or to apply professional judgement (Box 4). Where the data is inadequate, we then gather more or different data (Box 5). If the data is sufficient to apply the tools but we can't infer what causes the failure (Box 6) our next step depends on the level of certainty associated with the cause of failure.

Where we are uncertain about what causes the failure then we need to explore the situation by gathering and assessing more extensive data (Box 7). This might include increasing the number of biological elements sampled at the water body; it may include collecting more data on pressures.

Where we have a good idea what causes the failure (Box 8) then we would normally intensify monitoring focussing on the biological elements most likely to be affected by the pressure in question (Box 9). For example, where the suspected pressure is flow, invertebrate analysis might be taken to species rather than family level to improve the level of evidence linking pressure to failure. Occasionally, we might undertake an experimental application of a measure to reduce the pressure to demonstrate if this improves the biology (ie “Adaptive Management”) (Box 10).

Our knowledge of biological responses to pressures and our diagnostic toolkit will improve further as we repeat this process through time and at multiple water bodies.

Example guidance on the analysis of biological data in rivers

This appendix contains extracts of guidance given to Environment Agency Ecologists analysing data from rivers. It demonstrates the wide range of diagnostic tools available for a selection of biological elements (invertebrates, macrophytes and diatoms). Habitat assessment tools are also included as an example of supporting information used for investigations.

Introduction to ecological data


We collect a range of different ecological data from our rivers using a variety of different techniques. These data on biological quality elements (BQEs) will show responses to a variety of different pressures and are good indicators of environmental change and anthropogenic stresses.

How to look at data

Ecological data can be looked at in a number of forms:

  • Raw data

Most ecological data are in the form of taxa lists with an associated measure of abundance. Large amounts of information can be obtained from looking at these by looking at the ecological preferences of those taxa present. This can give an immediate indication of what pressures may be acting on the ecological communities.

  • Biotic indices

Most of the ecological data we collect can be summarised by biotic indices. They are designed to take a large amount of information and combine it into one number called an index or metric. They are very useful for summarising and presenting data but can overlook the extra information that can be gained from looking at the raw data. These indices are often targeted and describe the impact of specific environmental pressures.

Classification tools

Classification tools are generally designed to process biotic indices to make them comparable across river type, habitat and index type. The outputs from these tools are standardised and are in a format that makes them easy to understand, even by people with no experience of ecology. They are extremely useful for summarising data and presenting it in a regional or national context. The tools describe the quality of ecology against a standardised scale.

WFD biological classification tools

The classification tools referred to in this document are used by the Environment Agency, the Scottish Environment Protection Agency and Northern Ireland Environment Agency to carry out WFD reporting.

Environmental quality ratios (EQR)

The WFD classification tools are designed to calculate the current condition of a particular biological quality element (BQE). They do this by calculating an environmental quality ratio (EQR). This is achieved by comparing the observed value of the metric calculated from samples with the value of the same metric expected at WFD reference state. This is expressed as a decimal fraction of the observed value against the reference value.

Macroinvertebrate data


Macroinvertebrates have historically been used as indicators of organic pollution. More recently they have proved useful for assessing the impact of many other anthropogenic stresses. There are a variety of quantitative and semi-quantitative techniques used to collect samples from rivers, lakes and canals, but all these techniques have been standardised to make the data collected comparable.

Biotic indices

Macroinvertebrate samples collected using a standard three minute kick/sweep sample or airlift technique can be can be used to calculate the following useful biotic indices or metrics:

  • Biological Monitoring Working Party score (BMWP). This index is primarily used to monitor the impact of organic water quality, but will also show responses to toxic pollution, siltation, habitat reduction and reduced flows. BMWP scores cannot be directly compared across river types.
  • Average score per taxon (ASPT). This index is primarily used as an indicator of organic pollution. This index is directly comparable between samples collected from different river types and in different seasons.
  • Lotic Invertebrate Flow Evaluation (LIFE). This is used to determine the sensitivity of an invertebrates community to changes in flow. LIFE scores can be calculated from both family level or species level data but will often be more informative when calculated from species data.
  • The number of taxa (N-TAXA). This is a simple diversity index. It is a non specific index of environmental pressure and is useful when pressure specific indices such as ASPT and LIFE show no response.
  • Proportion of sediment-sensitive Invertebrates (PSI). This is a biotic index designed to describe an invertebrates communities sensitivity to sedimentation.

Other biotic indices. There are many other biotic indices available for summarising macroinvertebrate data sets. Each index is designed to describe a different reaction by the invertebrate community. The indices described above have either been or will be adopted by the ecology community and the WFD. If you choose to use other biotic indices for a specific purposes, it is important you check their background and validity before using them to make decisions.

Non biotic index information

Macroinvertebrate data collected using other techniques such as grabs, corers or Surber samplers for example, are generally not appropriate for use with biotic indices. However, these data tend to be more suited to quantitative analysis techniques. Possible analysis techniques are mentioned below:

  • Sample composition. The ecological preferences of dominant taxa and the relative proportions in which each taxon or species occur can give you a very good idea of habitat type and the pressures acting on the ecology community. If you have a number of quantitative samples collected from different sites or over time, then multivariate analysis techniques such as Principal Component Analysis can be very useful to differentiate differences that may be arising between your samples;
  • Indicator species. Often in depth analysis of full taxa lists are not required. Key indicator species can be used to tell you about what pressures and environmental influences may be impacting your invertebrate communities.

Tools for classification

There are a variety of tools available to help interpret and classify macroinvertebrate data and indices. They include:

  • The River Invertebrate Classification Tool (RICT) RICT calculates what the invertebrate communities would be like at reference state for any given site based on its physical parameters. It then compares the prediction with the actual results recorded from samples taken at the site and produces an environmental quality ratio (EQR) for each site. The EQRs are then used to produce a classification for the site and assign it to an ecological status with an associated confidence of class. This is the principal tool used to produce WFD classifications for invertebrate data.
  • The HydroEcological Validation tool (HEV) can be used to calculate predicted (reference) conditions for LIFE, PSI, ASPT and N-TAXA indices. HEV

uses observed sample data to calculate the ecological quality indices (EQIs) for all four of these indices. EQIs are a measure of how different the observed indices are from reference state. The HEV tool does not produce a WFD classification. The HEV tool is useful for examining the impact of many different pressures/stresses on macroinvertebrates at the same time as they can all be compared side by side.

  • River pressure diagnostic system (RPDS) and the River pressure Basian belief network (RPBBN). Known collectively as the artificial intelligence (AI) tools, these packages allow you to explore your raw data to identify water quality pressures that may be acting on a site.



Diatoms are principally used to monitor nutrient enrichment (eutrophication). However, they have also proved useful for monitoring sedimentation, heavy metal pollution and are now being increasingly used to describe the impact of acidification.

Biotic indices

Diatom samples collected using the standard benthic diatom sampling techniques can be used to calculate the following biotic indices:

  • Trophic diatom index (TDI). This index describes the nutrient preferences of a diatom community. In lake assessments you should use the lake specific TDI (LTDI) for your investigations.
  • Percentage motile taxa (%motile). This index simply gives a proportion of the taxa identified that are motile. Benthic diatoms can be heavily affected by light limitation. Light limitation can occur from excessive growths of filamentous algae or siltation. Motile diatoms tend to fare better as they are able to migrate to the surface of the smothering substance to reach the light.
  • Percentage planktonic taxa (% planktonic). This index simply describes the proportion of taxa identified as being planktonic. Higher values mean more of the diatom community are made up of planktonic taxa. This can indicate that flows are reduced or the river impounded.
  • Diatom acidity metric (DAM). This is a relatively recent index and describes the acidity of the environment within which the diatom community exists.

Non biotic index information

Heavy metals. Some species of diatoms, particularly the Fragilaria groups, have been identified as being particularly sensitive to heavy metal pollution and have growth abnormalities in the cell frustules. No index is available to summarise this pressure, but abnormal cells are recorded during analysis.

Tools for classification

There is just one tool available to help interpret and classify diatom data and biotic indices.

DARLEQ is a data classification tool that calculates what the diatom communities should be like at reference state for any given site based on its physical parameters. It then compares these predictions with the actual results recorded from samples taken at the site to produce an EQR. The tool then produces an ecological status class and associated confidence of class. This is the principal tool used to produce WFD classifications using diatom data.



Macrophytes (including aquatic bryophytes) have been used traditionally to monitor for the impacts of eutrophication in rivers. However, like invertebrates they respond to a wide range of pressures which can make the interpretation of macrophyte data less clear cut than with diatom data.

Pressures/ stresses

Macrophytes respond to a number of different pressures. However, different pressures can often have similar effects and so it can be difficult to apportion cause. Pressures that macrophytes show a known response to include:

  • Phosphate In freshwater environments, plants are principally restricted by the availability of the nutrient phosphorous. Increases in nutrients will often cause a change in the macrophyte community to one dominated by plants with a preference for high nutrient conditions.
  • Flows can have a significant impact on the macrophyte communities within a reach of river. If flows change then the plant community will often change in response. In lowland systems, flow pressures can often be masked by nutrient pressures.
  • Habitat modification. Plants respond both directly and indirectly to habitat modification.
  • Siltation. Siltation pressures tend to cause a decline in the diversity of the macrophyte community, with the silt loving plants becoming dominant.
  • Water level fluctuation. In lakes, where there are large and or rapid changes in water level, macrophyte communities can show significant response.

Biotic indices

Surveys carried out to using the standard WFD macrophyte survey methodology can be used to generate the following biotic indices:

  • Mean trophic rank (MTR). The MTR index describes a plant communities preferences to nutrients. The MTR scoring system has now been largely superseded by the RMNI;
  • Mean flow rank (MFR). The MFR index is very similar to the MTR however it describes a plant communities response to flow conditions. The MFR scoring system has now been superseded by the RMHI;
  • River macrophyte nutrient index. The RMNI is designed to categorise a macrophyte community‟s preferences to nutrient levels
  • River macrophyte hydraulic index (RMHI). The RMHI describe a plant community‟s preferences for flow conditions.
  • Number of aquatic plant functional groups (NFG). The NFG index is a richness or diversity index and describes the number of functional macrophyte groups existing within a surveyed plant community;
  • Number of aquatic taxa (NTAXA). The NTAXA index is another richness index and simply describes the number of truly aquatic taxa.

Both the NFG and NTAXA indices are very useful indicators of habitat quality. High quality habitats with good flow regime, habitat heterogeneity, upstream connectivity and low sedimentation pressures will have higher values for both these indices.

Tools for classification

The principal tool available to help interpret the different biotic indices calculated from macrophyte data is called LEAFPACS.

  • LEAFPACS is a data classification tool that calculates what the macrophyte communities should be like at reference state for any given site based on its physical parameters. It compares these predictions with the actual results recorded from surveys carried out at the site. This enables it to produce a classification of the ecological status of the site and associated confidence of class. This is the principal tool used to produce WFD classifications using macrophyte data.



River habitat survey (RHS) provides an assessment of the morphology of a 500m reach of river, recording both modifications and natural features, and giving an idea of habitat quality and diversity. Hydromorphology forms part of the overall ecology of a water body by underpinning and supporting the biology. Most aquatic species have certain physical habitat requirements, in addition to those of water quality and hydrology.


WFD requires the hydromorphology of a water body to be sufficiently high to support all of the biological quality elements. We assess hydromorphology to:

  • investigate reasons for failure of good ecological status or a deterioration in status;
  • assess the impacts of any proposed new modifications on ecology;
  • plan mitigation or restoration measures where necessary.


RHS survey data can be summarised using two summary indices.

  • The habitat modification score (HM) is a scoring system used to assess the degree of modification associated with a river. The HM score is independent of water body type and so can be used to describe artificial modification to physical structure across the board.
  • The habitat quality assessment (HQA) scoring system offers a broad measure of the diversity and „naturalness‟ of the physical habitat structure of a site, including both the channel and river corridor.

HM and HQA indices are designed to give only a summary of the habitat over the 500m river length surveyed. For more targeted investigations (such as looking at siltation), using the raw data is recommended.