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Water and its ecosystem functions

Work Package 1.2 - Water resources and flood risk management

Research Deliverable 
1.2.1 Water and its ecosystem functions
Leading Ideas 
Climate and the Environment


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.


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 continues in our farm sites and research catchments in continuing to develop an evidence base for Natural Flood Management (NFM) and water quality measures. Hydrology, hydrochemistry, sediment and habitat quality are being assessed across the River Dee and Lunan Water in Eastern Scotland in farmed landscapes, assessment of buffer strips at the Balruddery farm and in Tarland, peri-urban expansion effects on water quality in Elsick and morphology in the upper River Dee and Bowmont Water (Borders). These contribute to our long term understanding of processes and environmental change, support development of new techniques (in-situ sensors and pollution source tracing methods), allow us to integrate with on-the-ground stakeholders, follow management and take part in national strategies (for example Environmental Data Platforms).    

Plans for evaluation of improvements in habitat and ecological functioning following river restoration are developing in NE Scottish rivers. Pre-intervention baseline surveys of morphology, ecology and habitat will continue and will facilitate rigorous scientific assessment of the interventions now being realised for a tributary entering lower section of the River Dee. In the upper Dee assessment of 3-years of data and modelling of the impacts of a large restoration of floodplain connectivity along the main stem.

Sediment pollution sources, the behaviour in-stream and pollution carrying capacity of the sediments are key factors in river quality. Sediments also allow strong science links to catchment stakeholders since sediments are a very visual sign of river health, are related to actions on soil erosion and unite the mitigation measures combating pollution with water-sediment retention measures that form part of Natural Flood Management. One area of ongoing work in this subject looks at the utility of high frequency time-series data on sediment delivery from turbidity probes and new ways to query complex datasets and learn about system behaviour and transferability of calibrations of turbidity against wider parameters of interest (e.g. phosphorus). Another area is developing new tracers to source sediments based on patterns of organic matter imparted by the field crop that can inform on roles of certain land cover and management types in erosion.

Our emerging contaminants assessment work looks at microbial and organic chemical threats to water quality. Both groups of pollutants suffer from considerable areas of weak evidence for the occurrence and behaviour of directly-measured pathogens and chemicals and complex arrays of breakdown products in the environment. Ongoing microbial work is developing libraries of DNA analysed from water and environmental sources to compare to conventional monitoring via faecal indicator organisms, assess the prevalence of certain antimicrobial resistance genes and inform on better source management. Work between the James Hutton Institute and Moredun Research Institute focusses on both E Coli and Cryptosporidium and the data generated are starting to allow better catchment pathogen modelling. The presence of chemical contaminants of pesticides, pharmaceuticals are being assessed in sites in the River Dee, building on previous work in the River Ugie and being combined into risk assessments of exposure across freshwater to coastal systems. 

Selected Outputs




  • Stutter et al. (2018) Rethinking buffer strips in three-dimensions. Presentation at the CIWEM Diffuse Pollution: Policy and Practice conference, London.  The work presented detailed the integration of ideas across RESAS, EA, Danish and Irish EPA funded initiatives.
  • Bowmont catchment research summarised in chapter ‘Bowmont Catchment Initiative’ of "Engineering with Nature: An Atlas". Bridges, T. S. et al.  (2018) Engineering With Nature: an atlas. U.S. Army Engineer Research and Development Center.
  • Vinten, A. et al. (2018). Analysis of turbidity time series data from the Lunan Water catchment, Scotland, using Hidden Markov chains. Presentation at 3rd International Workshop on High Temporal Resolution Water Quality Monitoring and Analysis, Teagasc Agricultural College, Clonakilty, Co. Cork, Ireland, 12-13th June, 2018.
  • Teagasc, IST, Pagaling, E.; Abel, C.; Avery, L.; Belgrade, University of Surrey, City Analysts Ltd, GPS, Desing, Fruit and Veggies 'Suitability of novel technologies for determining irrigation, processing and bottled water quality'  Technical report for the European Commission CORDIS Project, Aquavalens, Cluster 3, WP12: Food production - Water used in Food Processing and Bottled Waters
  • Pagaling, E.; Palmer, J.; Avery, L. 'The distribution of AMR genes in freshwater in Scotland.' The Scottish Universities Life Science Alliance (SULSA) Antimicrobial Resistance Conference, Technology and Innovation Centre, Glasgow, 26-27 April 2018. (Poster)
  • Pagaling, E. (2018) Molecular methods for pathogen detection. Aquavalens (Protecting the health of Europeans by improving methods for the detection of pathogens in drinking water and water used in food preparation) Dissemination Workshop, Broadway House, London, 16 May 2018.  Oral presentation
  • Zhang et al (2018) Monitoring strategy, annual fluxes and risk assessment of emerging contaminants in a catchment scale. Presentation at Emerging pollutants in freshwater ecosystems. Water JPI 2018 Conference, 6–7th of June 2018, Helsinki, Finland