Water Framework Directive assessment: estuarine and coastal waters

How to assess the impact of your activity in estuarine (transitional) and coastal waters for the Water Framework Directive (WFD). The guidance is called Clearing the Waters for All.

This guidance is for activities in the marine environment up to 1 nautical mile out to sea.

Many activities need approval before they can go ahead. You must provide a Water Framework Directive (WFD) assessment as part of your application to the public body that regulates and grants permissions for your activity.

A WFD assessment helps you and your regulator understand:

Every water body has a status. The current status is set out in the 2015 RBMPs. It’s based on the condition of different quality elements in the water body, for example biology.

The WFD aim is for all water bodies to be at good status. In a WFD assessment you must show if your activity will:

  • cause or contribute to deterioration of status
  • jeopardise the water body achieving good status

This guidance updates and replaces ‘Clearing the Waters’, the previous WFD guidance for dredging and disposal activities in estuarine and coastal waters.

Carry out your WFD assessment in stages

A WFD assessment can have up to 3 stages. You may not need to complete all stages, depending on what you find at each stage. The stages are:

  • screening – excludes any activities that do not need to go through the scoping or impact assessment stages
  • scoping – identifies the receptors that are potentially at risk from your activity and need impact assessment
  • impact assessment – considers the potential impacts of your activity, identifies ways to avoid or minimise impacts, and shows if your activity may cause deterioration or jeopardise the water body achieving good status

In your WFD assessment you should consider:

  • all activities you’ll carry out
  • each stage of the activity, for example construction, operation and decommissioning
  • the water body your activity is in and all water bodies you could affect

Use catchment data explorer to find out which water body your activity is in and other linked water bodies it could affect.

Screening: exclude activities from scoping

You do not need to carry out scoping if your activity is low risk. Your activity is low risk if it’s:

  • a self-service marine licence activity or an accelerated marine licence activity that meets specific conditions
  • maintaining pumps at pumping stations – if you do it regularly, avoid low dissolved oxygen levels during maintenance and minimise silt movement when restarting the pumps
  • removing blockages or obstacles like litter or debris within 10m of an existing structure to maintain flow
  • replacing or removing existing pipes, cables or services crossing over a water body – but not including any new structure or supports, or new bed or bank reinforcement
  • ‘over water’ replacement or repairs to, for example bridge, pier and jetty surfaces – if you minimise bank or bed disturbance

If you carried out your activity during 2009 to 2014 (when evidence was collected for the 2015 RBMPs) and you have a WFD assessment, do not repeat it unless:

  • you’ve since changed how you carry out that activity, including method, size or scale, volume, depth, location or timings
  • there’s been a pollution incident since your activity was last carried out

Scoping: identify risks to receptors

At the scoping stage you must identify all your activity’s potential risks to each receptor. The receptors are:

  • hydromorphology
  • biology – habitats
  • biology – fish
  • water quality
  • protected areas

These receptors are based on the water body’s quality elements.

You must also consider invasive non-native species (INNS) at the scoping stage.

Scoping template

The scoping template (ODT, 24.2 KB) can help you record your findings. If you use it, send a copy to your regulator as part of your WFD assessment.


Hydromorphology is the physical characteristics of estuaries and coasts. It includes the size, shape and structure of the water body, and the flow and quantity of water and sediment.

Include hydromorphology in your impact assessment if your activity could have:

  • an impact on the hydromorphology of a water body at high status
  • a significant impact on the hydromorphology of any water body

Impacts on hydromorphology include changes to:

  • morphological conditions, for example depth variation, the seabed and intertidal zone structure
  • tidal patterns, for example dominant currents, freshwater flow and wave exposure

Use the water body summary table (MS Excel Spreadsheet, 208 KB) to check the hydromorphology status of your water body.

Also include hydromorphology in your impact assessment if the water body is heavily modified for the same use as your activity.

Use the water body summary table (MS Excel Spreadsheet, 208 KB) to find out if a water body is classed as heavily modified and for what use.

Biology: habitats

Include habitats in your impact assessment if the footprint of your activity is any of the following:

  • 0.5km² or larger
  • 1% or more of the water body’s area
  • within 500m of any higher sensitivity habitat
  • 1% or more of any lower sensitivity habitat

A footprint may be a temperature or sediment plume.

For dredging, calculate the footprint as 1.5 times the dredge area.

For WFD assessment purposes, higher sensitivity habitats are:

  • chalk reef
  • clam, cockle and oyster beds
  • intertidal seagrass
  • maerl
  • mussel beds, including blue and horse mussel
  • polychaete reef
  • saltmarsh
  • subtidal kelp beds
  • subtidal seagrass

Lower sensitivity habitats are:

  • cobbles, gravel and shingle
  • intertidal soft sediments like sand and mud
  • rocky shore
  • subtidal boulder fields
  • subtidal rocky reef
  • subtidal soft sediments

Use the water body summary table (MS Excel Spreadsheet, 208 KB) and Magic maps to find information on the location and size of WFD habitats. Read the Magic D17 Clearing the Waters for All user guide if you need help using the habitat maps. You should also use other sources of habitat information if available.

Biology: fish

You only need to consider fish if your activity:

  • is in an estuary and could affect fish in the estuary
  • is outside the estuary but could delay or prevent fish from entering the estuary
  • could affect fish migrating through the estuary to freshwater

Include fish in your impact assessment if your activity could impact on normal fish behaviour like movement, migration or spawning. For example, if your activity will lead to:

  • a physical barrier like a barrage or weir
  • noise or vibration
  • a chemical change like low dissolved oxygen across part or all of the estuary
  • a significant change to the depth or flow of the water body

Also include fish in your impact assessment if your activity could cause:

  • entrainment, for example fish drawn into mechanical plant like cooling systems or tidal turbines
  • impingement, for example fish trapped against debris screens

Water quality

Include water quality in your impact assessment if your activity:

  • could affect water clarity, temperature, salinity, oxygen levels, nutrients or microbial patterns continuously for longer than a spring neap tidal cycle (about 14 days)
  • is in a water body with a phytoplankton status of moderate, poor or bad
  • is in a water body with a history of harmful algae

Use the water body summary table (MS Excel Spreadsheet, 208 KB) to find information on phytoplankton status and algal history.

Include water quality in your impact assessment if your activity uses or releases chemicals, for example through sediment disturbance or building works. This is necessary when either the:

If your activity releases chemicals on the EQSD list and has a mixing zone, like a discharge pipeline or outfall, follow the Environment Agency’s surface water pollution risk assessment guidance. This is part of the Environmental Permitting Regulations guidance.

Protected areas

If your activity is within 2km of any WFD protected area, include each identified area in your impact assessment.

WFD protected areas include:

  • special areas of conservation (SAC)
  • special protection areas (SPA)
  • shellfish waters
  • bathing waters
  • nutrient sensitive areas

Use Magic maps for information on the location of protected areas within 2km of your activity. Read the Magic D17 Clearing the Waters for All user guide if you need help using the protected areas maps.

A regulator can extend the 2km boundary if your activity has an especially high environmental risk. If so, they will let you know and you’ll need to consider the potential impacts on protected areas further away.

Invasive non-native species (INNS)

Include INNS in your impact assessment if your activity could introduce or spread INNS to a water body.

Risks of introducing or spreading INNS include:

  • materials or equipment that have come from, had use in or travelled through other water bodies
  • activities that help spread existing INNS, either within the immediate water body or to other water bodies

Find out about existing INNS.

Impact assessment: consider impacts and mitigation

You must carry out an impact assessment for each receptor identified during scoping as being at risk from your activity.

Your activity can create pressures on the marine environment. The pressures-activities matrix will help you identify ways that your activity could affect the receptors.

Consider if there’s a pathway linking the pressure to the receptor. If there’s no pathway there can be no impact on the receptor and you do not need to carry out any further assessment of that receptor.

If there is a potential pathway you should consider if your activity, and the pressure it creates, may cause deterioration of the receptor.

Your impact assessment must describe how you will mitigate any identified impacts. Mitigation includes avoiding or minimising your impacts.

Tailor your assessment to your activity, location and the potential risk to the receptor. Higher risk, more complex activities with multiple impacts will need a more detailed assessment.

Include information about other activities that could affect the same receptors. These activities could be taking place now or be planned for the future. You must consider the effect of your activity together with these other activities.

Assess for deterioration

Deterioration is when the status of a quality element reduces by one class. For example, biological quality elements from good to moderate status. If a quality element is already at the lowest status then any reduction in its condition counts as deterioration.

Use catchment data explorer to find the status of quality elements in a water body.

Temporary effects due to short-duration activities like construction or maintenance do not count as deterioration if the water body would recover in a short time without any restoration measures.

If your activity may cause deterioration, either of the quality element or supporting habitat, you must explain how. Consider if the impact is:

  • direct and immediate – it will happen at the same time and place as your activity
  • indirect – it will happen later or further away, including in other linked water bodies

Explain if your activity is the sole cause of the deterioration, or whether other activities in the affected water bodies may together cause the deterioration

If your activity may cause deterioration, you must identify ways to avoid the impact. If this is not possible or practical, you must identify ways to minimise the impact. This can include changes to:

  • the materials or substances you use
  • the size or scale of your activity
  • ways of working and how you use equipment or services
  • when the activity happens and for how long
  • where the activity takes place

Assess for protected areas

You must consider the impact your activity may have on each protected area identified during the scoping stage.

If there is no pathway for the activity to affect a protected area, you do not need to carry out any further assessment. This may be because:

  • of the type of activity it is
  • it has the potential to cause an impact but does not link hydrologically to the protected area

If you identify a pathway from the activity to the protected area, you must consider what the area is protected for and show how:

  • your activity could impact on the protected area
  • you will avoid or minimise the impact of your activity
  • your activity will not affect the protected area objectives and standards in the RBMP

If your activity will impact on a Natura 2000 site (SAC or SPA) you should refer to the Marine Conservation Advice Packages. You may have completed a Habitats Regulations Assessment or similar. If so, make clear reference to it in your impact assessment of protected areas.

Assess for invasive non-native species (INNS)

If your activity could create a pathway that risks introducing or spreading any INNS, you must show how you will remove or reduce this risk. One approach is to prepare a biosecurity plan.

Jeopardising good status

Every water body has a target status that it’s expected to achieve by a set date. You must consider if your activity will jeopardise the water body getting to its target status.

Use catchment data explorer to find a water body’s target status.

Where this status is less than good, you must also consider if your activity will jeopardise the water body getting to good status in the future.

Status can be jeopardised by activities that:

  • reduce the effectiveness of improvement activities taking place now
  • prevent improvement activities taking place in the future

Improvement activities are commonly called measures. Where there are measures, show that your activity will not jeopardise them happening now or in the future. A summary of measures can be found in the RBMPs.

Jeopardising mitigation measures

If your activity is in a water body that’s heavily modified for the same use as your activity, show that your activity will not jeopardise the mitigation measures in place now or planned for the future.

Use the mitigation measures table (MS Excel Spreadsheet, 16.3 KB) to find the mitigation measures in a water body.

Article 4.7 defence

You may need to consider whether you meet the conditions in Article 4.7 if your WFD assessment shows your activity will either:

  • cause a deterioration in the status of a water body
  • jeopardise a water body achieving good status

Contact the Environment Agency for more information.

Submit your WFD assessment

Prepare a report with your findings for each stage of the WFD assessment. Send the completed assessment and any supporting information or evidence to your regulator as part of your application for permission to carry out your activity.

Keep your own records too.

Your regulator may need further information to be able to make a decision on your application. They will contact you if they need this.


Contact the Environment Agency if you need help with your WFD assessment.

General enquiries

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Telephone from outside the UK (Monday to Friday, 8am to 6pm GMT) +44 (0) 114 282 5312

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The impact of COVID-19 means you may experience some delays in responses.

Published 15 December 2016
Last updated 9 November 2017 + show all updates
  1. Updated water body summary table with the 2016 WFD classifications.

  2. Updated guidance and the water body summary table with links to new dataset guidance on the Magic website.

  3. First published.