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RD 1.2.1 Water and its ecosystem functions

IMage of lochan

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.

Further information

General information on the Scottish Environment, Food and Agriculture Research Institutes (SEFARI) and the Scottish Government funded Strategic Research Portfolio can be found on the SEFARI website.
Within this, there are webpages providing summary overview information for each of the Research Deliverables (RDs) within the Strategic Programme. The page for RD 1.2.1 Water and its ecosystem functions is available here and includes annual progress and highlights summaries, key outputs and links to case studies and key research staff.
To complement this, some additional information is provided below on specific Objectives and projects.

Contact Mark Wilkinson for more information generally about work in this RD.



The work comprises two objectives; O1: Evidence base for catchment processes: understanding the impact of Nature Based Solutions and O2: Contaminants of Concern: Sediment, pathogens & emerging contaminants. There are five ongoing core work areas associated with each objective with a number of research activities.

Objective 1a: Establishing an evidence base for NFM and rural SuDs (including Green Infrastructure)

This work will monitor and analyze water quantity and quality data relating to natural flood management and rural SuDs measures installed at contrasting scales (assessing the multiple benefits). For example, we will perform field experiments to demonstrate the utility of designer riparian buffer strips and gather evidence around the functioning of catchment based measures in the Dee and Lunan catchments.

Contacts: Helen Watson and Mark Wilkinson

Objective 1b: Effects of altered and restored river morphology on aquatic physical habitat and ecology

This research will support the Scottish Government/SEPA-led Pilot Catchments initiative (2015-27) by providing a detailed assessment of the ecological effects of morphological restoration, a key goal of WFD-led River Basin Management Plans. We will use existing long-term monitoring data (O1a) combined with targeted ecological studies to investigate the influence of catchment scale factors on the success of morphological restoration projects in achieving ecological improvements.

Contacts: Steve Addy and Susan Cooksley

Image showing flooded arable field

Objective 2a: Fine sediments: sources, impacts and management

The fine sediment research aims to deliver evidence to SEPA on the potential sources of fine sediments and associated contaminants. The work has three work activities:

  1. Sediment sources,
  2. Impacts, and
  3. Management

Contacts: Nikki Baggaley, Andy Vinten and Susan Cooksley

Objective 2b: Detection of the pathogen sources, mitigation and KE demonstration

Risk analysis and classifications, including link to future risk: The overarching aim of this activity is to develop our understanding of how sources of faecal pollution, methods for source tracking and pathogen behaviour relate to each other and the regulatory context of FIO measurements. Methods will be developed to enable the recovery and concentration of protozoan parasites from water samples and faecal samples derived from livestock and wildlife.

Contacts: Lisa Avery and Frank Katzer

Objective 2c: Understanding of environmental behaviour and effect of emerging contaminants by use of passive sampling and bioassay techniques:

This project aims to develop, optimise and apply novel monitoring techniques (passive sampling methods such as Polar Organic Chemical Integrative Samplers (POCIS)) providing time weighted average (TWA) concentrations, to understand the occurrence, transport and behaviour of emerging contaminants (e.g. pesticides, PPCPs and EDCs) from catchments (e.g. pesticides land application and WWTPs effluent) upon coastal waters.

Contact Zulin Zhang


The package of work provides critical empirical evidence to many work areas across the research programme such as modelling work in RD1.2.2, scenarios work in RD1.2.3 and guidance work in RD1.2.4. There are also strong links to all other work packages in Theme 1.

Example outputs from the research to date include both technical studies describing science development and those putting the work in the context of our working with key stakeholders such as SEPA, Scottish Water, SNH, Forestry Commission Scotland, Fisheries Boards, Estates and others. These can be further explored under each individual project page mentioned above.

Project Information
Project Type: 
Active Project
SEFARI – Scottish Environment, Food and Agriculture Research InstitutesSEFARI is the collective of six Scottish world-leading Research Institutes working across the spectrum of environment, land, food, agriculture and communities – all topics which affect how we live our lives, in Scotland and beyond.


Areas of Interest

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The James Hutton Research Institute is the result of the merger in April 2011 of MLURI and SCRI. This merger formed a new powerhouse for research into food, land use, and climate change.