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What is natural habitat function/natural ecosystem function?

Our most naturally functioning freshwater habitats are those with:

  • water chemistry that is not impacted by pollution;
  • natural morphology and dynamic physical processes shaping habitat mosaics;
  • a natural hydrological regime not impacted by abstraction, drainage and impoundments;
  • natural biological assemblages with a lack of invasive non-native species or other direct biological manipulations such as fish species removals and stocking.

These conditions generate high quality, dynamic habitat mosaics that provide niches for all of our native species, whether they are commonplace or rare. The Freshwater and Wetland Habitat Narrative provides more detailed explanation.

Standing waters of artificial origin can still function in this way and consequently can still be considered naturally functioning if they possess the characteristics above.


What are the priority river and lake habitat maps?

In England, rivers and lakes with high levels of naturalness that support characteristic species assemblages are now rare because so many have been modified or subjected to physical, hydrological, water quality or biological (e.g. non-native species) pressures. The priority river and lake habitat maps are intended to capture those water bodies judged to remain in a highly natural condition, based on the hydrological regime, water quality, physical morphology and biology stressors (particularly non-native species and fisheries management). The full reports for the priority river and lake habitats maps can be found on the Natural England website here: rivers and lakes. The current versions of the priority habitat maps can be viewed on this website, here for rivers; and here for lakes


What are the associated maps of river and lake restoration priorities?

The map of river restoration priorities shows rivers that are not sufficiently natural to include on the priority habitat map, but are of particular priority for restoration because they are examples of certain river types (chalk rivers and active shingle rivers) that are of particular conservation interest and limited spatial extent. This map needs to be refined to reflect local priorities for restoration of natural function, not necessarily connected to these certain river types.

The map of lake restoration priorities shows lakes that are not sufficiently natural to include on the priority habitat map, but are not far off that condition. Such sites may be most easily restorable to a level of natural function where they can be included on the priority lake habitat map.

The intention is that these maps will be refined with stakeholders to become a mechanism for highlighting local priorities for different sorts of restoration of natural habitat function – hydrological, physical, chemical and biological. Further information on how this will be done will appear on this website. Any site that falls under a specific habitat type included in the UK river and lake priority habitat definitions (e.g. chalk river or eutrophic lake), and therefore warrants specific consideration, can be highlighted as a priority for restoration action, if natural function can be restored.


Why are these maps needed?

Government recognises ‘habitats and species of principal importance’ for the conservation of biological diversity under Section 41 of the Natural Environment and Rural Communities Act 2006. Section 40 states that “Every public authority must, in exercising its functions, have regard, so far as is consistent with the proper exercise of those functions, to the purpose of conserving biodiversity”. Section 3 places a duty on the Secretary of State to “take such steps as appear to … be reasonably practicable to further the conservation of the ….types of habitat included in any list published under this section, or promote the taking by others of such steps”.

Efforts have been made to identify and map “priority habitats and species” in England, but this exercise was never completed for rivers and lakes, until now. The original mapping exercises were undertaken by the Centre for Hydrology and Ecology (CEH), Natural England (NE) and the Environment Agency (EA) on behalf of Defra and the Terrestrial Biodiversity Group which oversees the implementation of England’s Biodiversity Strategy (currently ‘Biodiversity 2020’). The maps will be used to prevent the deterioration of our most natural remaining rivers and lakes, and to focus work to restore natural processes where possible.


What are the objectives for priority river and lake habitats?

The broad aim is to protect our most natural remaining examples of freshwater habitats together with their associated wetlands, and restore as much natural function as possible to the rest of the freshwater habitat resource. This aim aligns with the spirit of the Water Framework Directive and freshwater habitat objectives for specially protected sites (Special Areas of Conservation notified under the under the European Habitats Directive and Sites of Special Scientific Interest notified under domestic legislation).

There will be greater scope to restore natural function in some places than others, and it is important to target the most effort at the places with greatest opportunity. The priority habitat maps help us to protect our most naturally functioning sites, whilst the maps of restoration priorities will (as they develop) help us to target restoration effort where it will be most fruitful.


What additional protection do the priority habitat maps afford a river or lake?

The priority river and lake maps add value to protection under the Water Framework Directive and the protected site series (Sites of Special Scientific Interest and Special Areas of Conservation) by providing additional recognition for our most natural rivers and lakes. This is important because headwater streams, riparian habitats and habitat naturalness have no explicit protection under the Water Framework Directive (even though their protection is implicit in the spirit of the Directive). Sites on the priority habitat maps are recognised in planning and permitting processes, where preventative measures will be needed to help protect priority rivers and lakes from further losses of naturalness and cumulative pressures.


How do these maps relate to the UK definition of priority river habitat?

The formal UK definition encompasses headwater streams, chalk rivers, active shingle rivers, and rivers with Ranunculion/Batrachion vegetation (EU Habitats Directive Annex I river habitat type), as well as rivers with certain priority species.

In England, a new mapping analysis has been undertaken, focussing on naturalness in recognition of the importance of natural processes in delivering sustainable river habitats that support characteristic assemblages of species. This is intended to provide much better alignment with the principles of the Water Framework Directive and the Sites of Special Scientific Interest SSSI notification process, both of which are based on protecting natural river habitat function as far as possible. This new approach was agreed by the Rivers Biodiversity Integration Group (as was) and endorsed by the Terrestrial Biodiversity Group as part of Biodiversity 2020 delivery.

The associated map of restoration priorities is intended to recognise that there are many more rivers and streams that fall under the specific habitat types listed in the UK priority habitat definition. This map provides a vehicle for ensuring that these rivers and streams are all highlighted as priorities for conservation action. The approach being taken to assessing the whole river habitat resource against priority habitat objectives ensures that the condition of all of these rivers and streams are taken into account.


How do these maps relate to the UK definition of priority lake habitat?

The formal UK definitions encompass all lakes. As lakes are rarely destroyed (unlike other habitats), but are severely degraded, such an approach fails to acknowledge that many of England’s lakes no longer support their characteristic biodiversity. Consequently inclusion of all lakes in the priority habitat definition does not enable decision making that values lakes which continue to support biodiversity.

In England, a new mapping analysis was undertaken, focussing on naturalness in recognition of the importance of natural processes in delivering sustainable lake habitats that support characteristic assemblages of species. This is intended to provide much better alignment with the principles of the Water Framework Directive and theSites of Special Scientific Interest notification process, both of which are based on protecting natural lake habitat function as far as possible. This new approach was endorsed by the Terrestrial Biodiversity Group as part of Biodiversity 2020 delivery.

The associated map of restoration priorities is intended to recognise that the lake priority habitat types cover all lakes. As such there is a driver to restore the natural function of all lakes. This map suggests which lakes may be most amenable to restoration, as we know their condition is not as impaired as others. However there are a large number of lakes, particularly small ones which we have no information on. Restoring the natural functioning of any lake contributes to the objectives for priority habitat.


How were the priority habitat maps developed?

Highly natural rivers and lakes have natural hydrological, nutrient and sediment delivery regimes; minimal physical modifications to the water body, banks and riparian zone; natural longitudinal and lateral hydrological and biological connectivity; an absence of non-native species and low intensity angling activities. Such rivers and lakes are now rare in the UK, with lowland rivers and lakes subject to a far greater range of pressures than those in the uplands.

The river map was developed through a national GIS analysis undertaken by CEH using data from NE and EA on the main components of habitat integrity:

  • hydrology (deviations from “natural” flow regime);
  • physical modifications (using the Habitat Modification Score from RHS, the number of in-channel structures and Flood Defence Assets);
  • chemistry (DO, ammonia, phosphate levels and pH); and
  • and biology (absence of non-native species).

Water Framework Directive waterbody status assessment was also considered. The 3 high ecological status and 11 high morphological status waterbodies in England were included, whilst artificial or heavily modified waterbodies were excluded from the maps.

The priority river habitat map also includes those headwater areas with the highest proportion of semi-natural land cover, as a proxy measure for naturalness because we lack direct data on such streams. As semi-natural land use is much more prevalent in the uplands, this has given a geographical bias in the results. This bias is somewhat misleading, as many upland streams have been degraded by moorland gripping and burning which generates heavy loads of organic particulates, whilst some upland areas suffer from a legacy of acid pollution and metal ore mining. Evaluation of the naturalness of headwater streams needs much more work, covering all types including rarities such as streams fed by tufa-forming springs.

A similar mapping exercise was conducted for lakes, although the limited amount of data available on much of the lake habitat resource severely hampered the analysis.


What are the limitations of the maps?

The original maps are necessarily relatively crude as they were developed using nationally available England-level datasets, mainly from the Water Framework Directive (WFD) at waterbody-level.

Whilst the GIS layer of the priority river habitat map is of high spatial resolution, the national analysis on which the map is based cannot discriminate differences in naturalness within a WFD waterbody. Even at waterbody-scale, data are patchy so there is considerable risk of anomalous judgements in this original map. In particular there is very little information available on the vast network of headwater streams across the country, including both naturally perennial and naturally intermittent stream habitat. These headwater streams have their own characteristic flora and fauna and are vital to the ecological well-being of larger river sections further downstream. An initial process of local refinement of the river map has been undertaken by statutory agency staff, using expert judgement, but this has only scratched the surface of the information gap in the headwater stream network.

The parallel mapping exercise for lakes identified a very large number of lakes without any available data, which needs to be addressed as a matter of urgency.


How will the maps be used?

The new priority river and lake habitat maps will help us to protect and enhance the most natural examples of England’s rivers and lakes from further impacts on natural habitat function, and will provide impetus to tackle whatever impacts on natural function these water bodies might suffer from. Use of these maps relates to achieving Outcome 1A of England’s Biodiversity 2020 strategy. The restoration priorities maps will help us focus efforts to restore natural river habitat function in the wider river network, to help meet Outcome 1B of Biodiversity 2020.

The maps will be used to help target agri-environment funding through the Countryside Stewardship Scheme and successor schemes. The Environment Agency will use the maps in River Basin and Catchment Flood Risk management plans and strategies, when planning capital schemes and maintenance programmes, and when determining applications for environmental permits. The maps will be vital for screening environmental permit applications to ensure the best rivers are protected from damaging activities, and when determining priorities for restoration action to meet Water Framework Directive objectives.

All biodiversity partners are encouraged to help refine and use the maps to highlight where special attention should be focused to protect or restore natural river and lake habitat function.


Why are rivers and lakes on the priority habitat maps worth conserving?

Natural river and lake habitat function provides the best and most sustainable expression of characteristic biological communities associated with rivers and lakes, and generates conditions that provide greatest resilience to climate change. There are very few remaining near-natural rivers and lakes in England.

The majority of rivers (by length) lie within the headwater stream resource which is not well-protected by either the Water Framework Directive or the designated site network. Most of our lakes are relatively small and not included as waterbodies under the Water Framework Directive (WFD). The priority habitat maps will help us to protect and enhance these watercourses beyond what could be achieved through SSSI protection and measures to achieve ecological status objectives under the WFD.


Why do the priority river and lake habitat maps need refining?

If the maps are to be effective in influencing decision-making over new developments and restoration activities, they must reflect local knowledge of where our most natural remaining sites are. We know inadequate data led to considerable limitations in the original version of the maps; if they were left unrefined local operational decision-making would not be as effective as it could be.

These maps will be refined using the data contributed to the data portal.


Some of the rivers on the original priority habitat map are not very natural at all – how can that be?

The national analysis used a structured approach to the available data and tried to select Water Framework Directive (WFD) waterbodies that were close to what might be considered high ecological status, but falling short on one component of habitat integrity (e.g. physical habitat, hydrology, water quality) by no more than what might be considered good ecological status. If a poor quality river section or stream is currently on the priority habitat map it is either an artefact of the nationally available data or the way in which the data have been aggregated. Data for an attribute that would otherwise downgrade the waterbody may have been missing. Alternatively, a degraded river may be part of a WFD waterbody that is otherwise quite natural, in which case it would be allocated the naturalness of the wider waterbody. In other words, there are anomalies on the map that still need to be addressed through local refinements.

If this is the case, contribute data to the data portal so your knowledge of the site can inform the next iteration of the map.


Some very natural rivers and lakes that I would expect to see on the priority habitat map are not there – why?

This is probably because of missing data in the original analysis of nationally available data. If there were no data to score a key component of naturalness, the waterbody wouldn’t have received an overall naturalness score and therefore could not go on the map. For rivers it may also be because a quite natural tributary is a part of a wider waterbody that is otherwise not sufficiently natural to have been included on the original version of the map. For lakes many sites have no data at all on which to make a naturalness assessment and so cannot currently appear on the map.

We would like to know more about these sites. Please contribute your data on these sites through the data portal so it can inform the next iteration of the map.


Will future refinements of the maps only consider whole Water Framework Directive waterbodies?

No. There may be very natural tributaries within a waterbody that is otherwise not sufficiently natural to be included on the priority river habitat map – these should be identified and included wherever possible. We recognise that there are serious limitations around what we know of smaller rivers and streams that are not subject to WFD monitoring.

Many smaller lakes will not be defined as a WFD water body and yet can still be considered lake priority habitat. Such lakes should be identified and included where possible.


How does the identification of small water bodies dotted over the landscape promote catchment-based management?

Catchment management has to be built up from an understanding of the detailed needs of habitats within a catchment. Developing priority river and lake habitat maps in this way is no different to understanding the ecological status of different Water Framework Directive water bodies or of different protected sites in a catchment. Catchment management planning is about integrating such information and building the best management framework possible.


None of the water bodies in my area seem to be sufficiently natural to be included on the priority habitat map – does that mean rivers and lakes aren’t a priority in my area?

Some areas of England have very little in the way of natural water bodies left, and that’s just a fact of life. However, there may be headwater streams or small lakes or ponds tucked away that have escaped notice, particularly those within terrestrial Sites of Special Scientific Interest or other semi-natural habitat (particularly ancient woodland). If the larger water bodies of your area are not sufficiently natural, there may well be hidden gems in the smaller water body network – in areas where they have been looked for they have generally been found, even in unlikely parts of lowland England.

Even if you have no highly naturally functioning habitat left in your area, you can still identify local restoration priorities for restoring natural function. By contributing your data on these sites through the data portal, they will inform the next iteration of the restoration priorities map (see the associated maps of river and lake restoration priorities here).


A river or lake Sites of Special Scientific Interest (SSSIs) in my area isn’t on the priority habitat map – why?

Freshwater Sites of Special Scientific Interest (SSSIs) would only be suitable for inclusion if they meet the level of naturalness that we would expect to be included on the priority habitat maps. Freshwater SSSIs are dealt with through a separate target in Biodiversity 2020 so there is no need to worry about their priority level – they are already a priority for protection (and restoration where necessary). The focus of the freshwater priority habitat work is on non-SSSI freshwater habitat.


Why are so many examples of river and lake types that are included in the UK priority habitat definitions not included in the priority habitat maps for England?

If all the examples of all river and lake types included in the UK priority habitat definitions were shown on the priority habitat maps, nearly all rivers, streams and lakes in England would be on the maps. We needed a way of working with the UK definitions and coming up with a subset of the total habitat resource that comprised our most ecologically important sites. The only rational basis for doing this was to use naturalness and natural habitat function. This approach has generated a common language between the main drivers for river habitat conservation – the Water Framework Directive, Sites of Special Scientific Interest/Special Areas of Conservation notification, and priority habitat. Sites not included on the priority habitat map are not forgotten – they are considered within the associated restoration priorities maps.


How will priority habitat condition be assessed and reported?

Proposals have been developed for a coherent monitoring and assessment framework for priority river, lake and pond habitat objectives. These build on the foundation of Water Framework Directive (WFD) and protected sites (Sites of Special Scientific Interest and Special Areas of Conservation) monitoring and add in other monitoring programmes (such as Countryside Survey) to build a representative picture of natural freshwater habitat function across the habitat resource. Proposals include habitat function attributes (such as lateral and longitudinal connectivity), assessment of neglected habitats (such as the riparian zone) and small waterbodies to provide a more holistic picture of habitat condition than is possible through WFD assessment.

There are various strategic reviews of monitoring and assessment of habitats taking place at present and it is not clear how the proposals for priority freshwater habitats will be progressed. It is hoped that the naturalness assessments developed for the citizen data portal on this website will be able to serve as a citizen science contribution to the assessment of the habitat resource, albeit contribution with limited technical confidence.


What percentage of rivers and lakes are a priority?

This is not an easy question to answer, not least because it depends on the spatial resolution of observation (i.e. which map scale is being considered). The priority habitat maps contain relatively few rivers and lakes, comprising a low percentage of the total habitat resource. This said, the priority habitat map for rivers also includes a larger number of headwater areas, where the specific streams that are worthy of being on the map are unknown. For lakes there is a very large number of lakes with no data, some of which will be added to the priority habitat map as our knowledge improves.

There is a considerably greater proportion of the river network on the map of river habitat restoration priorities, reflecting the degree of modification to which England’s rivers have been subjected. Whilst there are relatively few lakes on the parallel map of lake habitat restoration priorities, this number will increase as our knowledge improves. Work is needed to refine the maps of restoration priorities so that they better reflect local priorities for restoration based on what is feasible.


Shouldn’t biodiversity hotspots be included on the priority habitat maps?

We want to conserve all native freshwater species (including priority species) within naturally functioning freshwater ecosystems wherever possible. Natural river and lake habitat function provides suitable conditions for supporting all of our native freshwater flora and fauna within a dynamic and complex habitat mosaic. Individual species may be present at a location, or found in abnormally high abundance, because of artificial modifications to the habitat (e.g. impoundment, eutrophication, flow modification). We need to ensure that we do not create conflicts between conserving species where they are currently located and conserving them in naturally functioning habitat mosaics.

The priority habitat maps and the distribution of biodiversity hotspots are therefore different but linked perspectives on freshwater conservation. Where they coincide the two are compatible and we can protect and restore natural ecosystem function with confidence. Where they do not coincide careful planning is needed for any measures to restore natural ecosystem function, to ensure that we have a strategy for protecting species rarities. Further explanation of this relationship is included in the freshwater and wetland habitat narrative.


What is the relationship between the priority habitat maps and other conservation designations?

River and lake Sites of Special Scientific Interest (SSSIs) and Special Areas of Conservation (SACs) that are designated for their habitat do not necessarily feature on the priority habitat maps because of impacts on their naturalness. River and lakes are designated SSSI/SAC as best (most natural) examples of their type, and in many cases river and lake types are uniformly affected by modifications such that there are no remaining highly naturl examples left in a given area. Measures are being taken to restore the chemical, physical, hydrological and biological naturalness of river and lake SSSIs and SACs, driven by Defra targets to restore the SSSI/SAC series to favourable condition.


How will the priority habitat maps be updated?

Anyone can contribute information on the naturalness of any stream/river or lake section in England via the ‘Citizen data portal’ on this website. New information will be reviewed at regular intervals and decisions will be made about which sites to add to the maps and (where needed) which to remove. This process will be overseen by Natural England, in collaboration with the Environment Agency, and Natural England will release new versions of the maps. The aim of the updates will be the same as the aim of the original national data analyses that generated the original maps, i.e. to capture highly natural sections of river and stream. Data will be screened to ensure that there is adequate confidence in assessments prior to changing the maps.


What quality assurance measures will be applied to data added to the Citizen data portal?

At present, all data added by stakeholders will be displayed on the mapping facilities on the website. This ensures that everyone’s contributions are properly recognised and each contributor can see that their assessments have been captured by the portal. In the future it is hoped that we will be able to introduce a simple data approval process to increase the confidence we have in the data on the portal. This would be based on approved local mediators and will depend on volunteers to take on this role in different parts of England.


How do I know if the site I want to assess is already on the priority habitat map?

Go to the citizen data portal (Rivers data or Lakes data depending on your interest) and you will be able to zoom in on the priority habitat map and see if your site is included.


How will the maps of river and lake restoration priorities be taken forward?

The plan for these maps is to work with national and local partners to develop a shared understanding of priorities for restoring natural function to the river and lake habitat resources. This will require consideration of both the need for such restoration and the practical scope and opportunity for it. Contributions to the citizen data portal will form part of the evidence base for this collaborative work.

Further information on how these maps will be refined will appear on this website. Any site that falls under a specific habitat type included in the UK river and lake priority habitat definitions (e.g. chalk river or eutrophic lake), and therefore warrants specific consideration, can be highlighted as a priority for restoration action, if natural function can be restored.