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Water and its ecosystem functions

Work Package Water resources and flood risk management

Research Deliverable 
Water and its ecosystem functions


River basins support nature, human life and economies in many ways, however, problems arising from agricultural and urban land use and, increasingly, climate change pose a range of management challenges. Pressures on our catchments include organic and inorganic pollution, flow and morphology alteration, flood risk, surface and groundwater abstraction, land use change, climate variability and change, invasive species and pathogens. There is a need to understand how these pressures affect the biophysical and ecological processes within our catchments. This RD focuses on understanding how the biophysical and ecological processes within water bodies operate and contribute to the delivery of ecosystem functions and health.

The Water Framework Directive (WFD) requires targeted measures to improve ecological status whilst the Habitats Directive requires that water Special Areas of Conservation attain and maintain Favourable Condition. There is an ongoing need for SEPA’s monitoring strategy for River Basin Management and the strategic research to be underpinned by effective statistical methods and associated sampling and instrumentation. Coupled with this, the EU Floods Directive (FD) requires governments to adopt, where possible, a sustainable approach to flood risk management. Natural flood management (NFM) is a sustainable approach to flood risk management being adopted in the Scotland, however, there is not enough evidence for the effectiveness of the various measures to allow it to be fully utilised by practitioners. RD 1.2.1. is contributing to key research evidence and synthesis in areas identified by SEPA, Scottish Government and the Environment Agency and driven by legislation pertaining to the WFD, Nitrates Directive, Drinking Water Directive, Flood Directive and Habitats Directive.

Aim of Research

To understand how  pressures such as problems arising from agricultural and urban land use and, increasingly, climate change affect the biophysical and ecological processes within our catchments.  The focus of the research is on understanding how the biophysical and ecological processes within water bodies operate and contribute to the delivery of ecosystem function and health. The core of this work will provide information and knowledge that is needed to address one of the fundamental research questions of the programme (How do Scotland’s natural assets function, how healthy are they, what are their trends, and what are ‘safe’limits to their sustainable use) and the issues of change, adaptation and management which are covered in other parts of the programme.


2021 / 2022
2021 / 2022

Continuing work from year 5 contained two strands of work. 1)  Post-restoration ecological survey of the Beltie Burn. This now means our empirical database now contains pre- and post-change data and allows the programme to conclude with a strong empirical evidence database. At Beltie, emerging patterns show significant changes to the biological community that are linked with the restoration intervention. 2)  The microbial research investigated source tracking specific faecal indicator organisms in the environment. Here, national datasets showed positive and negative relationships between land use characteristics and microbial parameters including FIOs, source tracking indicators, diversity indicators and antimicrobial resistance genes.

Also, this year several smaller projects took place. Final summaries were produced of core catchment management case studies. This included a final set of data collected from the Logie burn river restoration site.  Completed work also included using the Tarland model outputs translating soils to a set of hillslope-riparian contexts for which a 16-measure database have been shortlisted to more/less suitable per landscape type. We have produced datasets on the greenhouse gas emissions and soil nutrient dynamics of a range of monocot and dicot species both in the field and in mesocosm systems. A sampling campaign in the River Dee was conducted for the emerging contaminants monitoring particularly for the PPCPs (pharmaceutical and personal care products). The dataset suggested that the further investigation including more frequent monitoring and more new compounds were needed to further understand the contamination caused by emerging contaminants in Scottish rivers.


  • The Beltie Burn ecological surveys undertaken in 2021 are the first samples collected since the restoration intervention and represent the first 6 months of change to the biological community. Based on the robust sampling strategy, emerging patterns show significant changes to the biological community that are linked with the restoration intervention.
  • E. coli genome clustering was undertaken in a livestock dominated catchment. National scale data demonstrated a number of positive and negative relationships between land use characteristics and microbial parameters.
2020 / 2021
2020 / 2021

We continue to strengthen our empirical evidence and understanding of the various biophysical and ecological processes within water bodies. Increased sampling for emerging contaminants has been undertaken to try to detect possible impacts of Covid-19 on water quality. Monitoring of riparian buffer strips showed accumulations of available carbon, nitrogen and phosphorous, with differences of soil nitrate, carbon and phosphorous availability and nitrous oxide emissions between buffer strips. Those buffer strips dominated by grasses emitted more greenhouse gases than those with a wider range of species which instead tended to accumulate more phosphorous in the soil. Further progress evaluating the benefits of river restoration has been made.  For example, restoration work on the Beltie Burn was completed in late 2020 and a post-restoration topographical survey was undertaken.  Additional flow and water quality monitoring equipment was also added to the site to measure other responses to restoration.  These and other examples have led to several publications and policy/practice presentations.

Our microbial research methods using source tracking of the pathogens within catchments, will aid understanding environmental transmission and help in devising mitigation strategies. We applied bioinformatics and statistical approaches to analyse relatedness of genome sequences of E. coli isolates from a rural sub-catchment and demonstrated that some E. coli from livestock reach water courses, but others present in water courses have come from different sources. Cryptosporidium oocysts need to be concentrated before DNA extraction to allow speciation and genotyping using DNA based technologies. Moredun developed and established techniques to concentrate and detect Cryptosporidium oocysts from vegetation and sediment. Both approaches will aid source tracking of the pathogens within catchments, understanding environmental transmission and will help in devising mitigation strategies. All field campaign samples have been completed for the chemical contaminants analysis in the River Dee. Overall comparison of the measured concentrations from the two sampling methods (spot and passive sampling) is within the same magnitude for most of the analytes. The results showed that the concentration of contaminants, for example of an individual pesticide, was well below the EU permitted concentration value of 0.1 µg/l. The risk assessment (RQ, risk quotient) showed that most of contaminants were minimal to low risk to the aquatic environment although there were some exceptions. Relevant papers were published.


  • RESAS research on natural flood management (NFM) informs a UK Government POSTnote on ‘Natural mitigation of flood risk’. A briefing by the UK Parliamentary Office for Science and Technology was published recently delivering the key messages: a) NFM delivers other co-benefits, b) NFM is useful in relation to smaller more frequent floods and can be a relatively low-cost option, and c) NFM should often be used in conjunction with other approaches.  The briefing included RESAS research ranging from physical to social sciences.
  • A large-scale monitored river restoration project is underway. The Beltie Burn in Aberdeenshire was channelised and embanked in the 1800s, resulting in poor habitat and floodplain disconnection. The restoration works were completed in September 2020. One of the most significant river restoration projects in Scotland, the project is the subject of a high-quality monitoring study. The restoration is being led by the Dee Catchment Partnership and funded by NatureScot’s Biodiversity Challenge Fund.
  • Flood embankment lowering and natural recovery helps to restore natural connections between a river and its floodplain.  A 70 m long flood embankment on the upper River Dee in Aberdeenshire was lowered in 2015 to restore habitat and floodplain connectivity.  Two years of pre- and three years of post-restoration monitoring detected positive responses (paper here).   The monitoring demonstrated that improved river to floodplain connectivity can result from targeted flood embankment lowering and letting the ‘river do the work’.  Both the embankment lowering and natural changes in river shape due to a series of large floods resulted in large changes to floodplain connectivity.  Floodplain water tables rose by 4-9 cm on average, the river flow required for spillage onto the floodplain lowered by 55% and the frequency of floodplain spillage doubled.  Such approaches could help to improve catchment resilience to climate change by improving water storage and, hence reduce moderate floods downstream and help maintain baseflows during droughts. 
2019 / 2020
2019 / 2020

Field work and data collection continues to underpin catchment-based research. Monitoring of riparian buffer strips continues to show differential soil nitrate availability and nitrous oxide emissions between buffer strips with different plant community structures. Buffer strips dominated by grasses tend to emit more greenhouse gasses than those with a wider range of species including dicots. Studies at two river restoration sites are establishing a strong evidence base for the benefits of floodplain reconnection, re-meandering & dead-wood placements. The Beltie Burn study has achieved the data threshold required for effective statistical evaluation, representing one of the most comprehensive evaluations of a restoration project in Scotland; the groundworks for the restoration will be undertaken this summer. The Logie Burn monitoring dataset was updated and seven years post-restoration, the stream has gained sediment and pool habitat. 

A novel application of a statistical method for analysing stream water quality time series has been developed. This has been shown to improve the prediction of stream sediment phosphorus from high frequency turbidity measurements. We have also analysed stream and source samples for tracers which represent both soil and vegetation characteristics and can be used to indicate the sources of stream sediments. The application of source tracking methods to the National Waters Inventory DNA archive was completed and whole-genome sequencing carried out on ~500 E. coli isolates from Tarland sub-catchment sampling.  River sampling campaigns have been conducted and samples were measured for emerging contaminants.


  • Flood risk scientists co-develop an international workshop in Edinburgh. Working with SEPA, EA and Scottish Government, SEFARI scientists co-organised the international Nature Based Solutions (NBS) symposium in Edinburgh on May 2019. The event consisted of keynote speeches, including an opening address by Rosanna Cunningham, field trips and workshop sessions. The aim was to share international best practice around implementing NBS measures within catchments and on coasts to reduce flood risk and provide wider ecosystem services. Over 90 participants attended from 14 countries.
  • Collaboration strengthened with applied research in Ireland. SEFARI researchers presented multiple aspects of RESAS-funded research at the Catchment Science 2019 Conference (Wexford, November 2019), including modelling of phosphorus sources and mitigation; the F-MAPT tool to enable placement of flood mitigation measures; riparian management; water payment for ecosystem services and soil erosion work . Researchers are working closely with the Teagasc Institute and the Irish EPA in riparian and Natural Flood Management (NFM) allied research projects with mutual benefit for the land.
2018 / 2019
2018 / 2019

We continue to monitor within our catchment experiments at a variety of scales. Evidence collected from this RD has been published in international books and high impact scientific papers. A summary paper has been published highlighting how Natural Flood Management helps to mitigate flood flows at the local scale but highlights challenges and future directions for upscaling the approach to larger catchments and larger events. New statistical methods have led to improved understanding of the relationships between river flows and sediment and phosphorus in rivers. Also, research continues to take place on microbial source tracking by culture dependent and independent approaches which is key to understanding where faecal pollution is being generated and what and who is required to mitigate it. Research continues to investigate the occurrence and behaviour of emerging contaminants by developing monitoring and detection methods towards eventual improved modelling capabilities.


  • Scaling up Natural Flood Management: A summary paper has been written which highlights how NFM can help to mitigate flood peaks at the local scale through two case study examples. The issue of upscaling to large catchment areas is also discussed.
  • Buffer strips seminar: A presentation was given by a SEFARI scientist at the Chartered Institute of Water and Environmental Managers (CIWEM) diffuse pollution conference, London, 18-19th July entitled ‘Rethinking Buffer Strips in 3-Dimensions’ including international co-authors, EA and Forest Research (available here). The talk discusses how we can optimise the traditional grassed buffer strip to deliver more ecosystem services.
  • Bowmont research features in international book: The Bowmont catchment research has been recently summarised in a chapter of an international book published by the US Army Corp of Engineers. The book is called "Engineering with Nature: An Atlas" and gives an visual overview of natural flood management measures including tree planting and use of novel wooden structures in the catchment case study.
  • Presentation on turbidity: A paper presented at the 3rd International Workshop on High Temporal Resolution Water Quality Monitoring and Analysis (Clonakilty, Ireland) detailed statistical methods developed to look for ‘states’ (indicative of periods when changes occur in dominant controlling factors) in river monitoring data. The techniques improve how we use in-situ turbidity sensors to derive river sediment time-series using data from the Lunan catchment, Scotland, in a collaboration between researchers at James Hutton Institute and BioSS.
  • DNA approaches for understanding river microbial pollutants: A large database of E. coli isolates from NE Scotland catchment (livestock faeces-derived from soils, streamwaters, sediments) are completing being genetically sequenced to evaluate strains/characteristics passed from livestock to waters and help develop mitigation.  Antimicrobial resistance gene profiles from 50 of the isolates are showing novel multi-drug resistance.
2017 / 2018
2017 / 2018

This RD continues to provide empirical evidence to real world problems via applied research in catchments. These include assessing the impact of Natural Flood Management actions managing flood peaks using landscape water retention and in-stream techniques, to the identification of emerging contaminants using microbial (e.g. antimicrobial resistance genes) and chemical analyses (pesticides and pharmaceuticals). Scientific summaries from the Bowmont catchment have appeared in National documents which have been promoted by UK policy. Data and analysis in this RD have been supporting the production of high-quality scientific publications. Work on pathogens continues to improve our understanding of sources of specific target pathogens, not just indicator organisms, leading to improved environmental source-tracking, behaviour knowledge and eventually management. Continued research is closely being discussed with stakeholders (e.g. SEPA, SG) through mechanisms such as the flooding and diffuse pollution working groups.


  • Effect of Agriculture on the Environment: A set of special sessions at the Land Use and Water Quality Conference in the Hague in June 2017 were organised by the James Hutton Institute and Aarhus University. Presentations included work on buffer strip management, and will appear in a special collection of scientific papers in the Journal of Environmental Quality. Key highlights included the need for engagement with farmers to ensure effective mitigation measures.
  • Emerging contaminants assessed in a Scottish river and coastal waters: The annual flux and risk of emerging contaminants were estimated for a Scottish priority catchment (River Ugie) and to the adjacent estuary and North Sea and a research paper on this topic has been published.
  • Natural flood management in the Bowmont Water highlighted as a national case study: Outputs from the Bowmont Natural Flood Management study have featured as a case study in the recently published “Working with natural processes: evidence directory” (produced by the Environment Agency).
  • SRP research on multiple benefits of riparian buffer strips is developing international collaboration: Developed expertise examining riparian functions (pollutant mitigation, habitat, flood benefits and improving riparian condition and resilience) in Scotland has led to WP1.2 researchers partnering Irish researchers on a 4-year buffer design and placement project (Irish EPA funded; 2018-22) involving KE with Scottish stakeholders (SEPA, SNH) and another buffer design contract with the EA.
2016 / 2017
2016 / 2017

This RD has maintained continuity in evidence gathering and tool development around catchment studies in both research sites and 'real world' catchments. An example is the Tarland research catchment (headwater of the River Dee) being used to develop the partnership approaches for Natural Flood Management and morphological improvements and long term RESAS-funded catchment datasets have been uploaded onto NERC's open access datacentre. The River Dee has provided a large river context for integration of research evidence into environmental decision making (supporting the development of ecological monitoring for river restoration assessment, post flooding management responses). As a technical assessment and demonstration site we have used Balruddery farm to evaluate riparian and field-edge buffer management experiments to investigate multiple benefits of nutrient retention and cycling, biomass generation and habitat imnprovement set in the context of a working farm with demonstration examples utilising the industry events often hosted there. New tool development has focussed on methods for emerging water contaminants  (using and developing techinques for organic chemicals reported in a Nature journal in 2017) and on environmental tracers for sediments and pathogens. The data collected in this RD underpins the modelling in RD1.2.2.


  • Collaboration between JHI, CEH and SEPA (Willie Duncan) has resulted in closer integration of activities within RESAS WP1.2 and SEPA’s river restoration pilot program.
  • A paper on integrating the requirements of the Floods Directive and Water Framework Directive was presented to the European Commission Common Implementation Strategy.
  • A paper has been published in Nature: Ecology and Evolution, as part of international collaboration. The paper reports extraordinary levels of organic pollutants that persist in the endemic amphipod fauna from two ocean trenches. The study uses techniques developed in WP1.2 and reports contaminant levels were considerably higher than documented for nearby regions of heavy industrialization, indicating bioaccumulation of anthropogenic contamination. Jamieson et al. 2017 Nature: Ecology and Evolution.
  • RESAS work supported post-flood surveys of Storm Frank on the River Dee aiming to evaluate the scale of change and management lessons for future large floods (in Partnership with SEPA, Aberdeenshire and City Councils and MDT)

Future Activities

Work has concluded in RD1.2.1. However, many strands of this RD will now inform the next RESAS programme. There are two projects which will in part build on research funded in this programme, these are the Achieving multi-purpose Nature-Based Solutions project and Emerging Water Futures Projects.

Selected Outputs