Overview

Freshwater ecosystems in the Highland region are under stress from rising temperatures, altered rainfall patterns, and more frequent droughts and floods. These pressures are degrading water quality, reducing habitat suitability for sensitive species, and threatening the region’s renowned salmon and pearl mussel populations. Risks are intensifying, with warmer, drier summers, and heavier winter rainfall disrupting ecological balance, accelerating erosion, and encouraging the spread of invasive species. Climate change adaptation measures are emerging, including riparian (river bank) woodland restoration, improved catchment management, and enhanced monitoring, but current efforts remain fragmented and under-resourced. Coordinated regional collaboration will be essential to build resilience, protect ecosystems, and safeguard the economic and cultural value that Highland rivers and lochs provide to communities now and in the future.

 

What is the current level of risk?

Freshwater ecosystems across the Highland region are already showing clear signs of stress linked to the changing climate. Rising summer air and water temperatures have been recorded through the Scotland River Temperature Monitoring Network, causing thermal stress to cold-water species such as Atlantic salmon and trout, which are poorly adapted to warmer conditions. Fisheries Management Scotland now advises anglers to cease fishing when river temperatures exceed 18°C. Prolonged high temperatures and reduced flows have combined to cause mortality among freshwater pearl mussels in Highland rivers.[1] Low flows and drought events reduce oxygen levels, hinder fish migration, and increase disease susceptibility.[2]

Extreme rainfall and flood events are becoming more common, increasing sediment loads and destabilising riverbanks, particularly where invasive riparian plants such as Himalayan balsam die back seasonally. Together, these pressures are degrading water quality and habitat condition.

Climate change is altering Highland lochs through rising water temperatures, shifts in rainfall intensity, and changes in flushing rates, which together are driving more frequent algal and cyanobacterial blooms and degrading water quality. Deeper Highland lochs, such as Loch Ness, are experiencing earlier and longer periods of thermal stratification, leading to reduced deep-water oxygen levels and increased nutrient release from sediments, with knock-on effects on biodiversity and ecological condition.[3]

 

 

In the Highland region, catchments with limited riparian vegetation, such as parts of the Spey, Conon, and Oykel catchments, are particularly exposed to these changing conditions, as reduced shade exacerbates rising water temperatures and increases algal growth. Rising air and water temperatures are expected to drive further declines in dissolved oxygen, increasing stress and mortality in sensitive cold-water species, including salmon and freshwater pearl mussel. Warmer, drier summers and altered hydrological regimes are shifting aquatic plant and invertebrate communities, favouring more thermophilic (heat-tolerant) species and altering food-web dynamics.[4] Increased nutrient concentrations during low-flow periods, coupled with higher temperatures, are contributing to more frequent algal blooms and reduced dissolved oxygen levels in standing waters, which can damage aquatic ecosystems, harm fish populations, and degrade overall water quality.[5] These cumulative effects are weakening the ecological integrity of Highland freshwater ecosystems, threatening species reliant on cold, well-oxygenated conditions, and undermining the region’s reputation for high-quality waters that support biodiversity, recreation, and rural livelihoods.

Economic losses linked to climate-induced disease and temperature stress in the salmon industry are estimated in the tens of millions of pounds annually, with implications for rural employment, angling tourism, and wider supply chains that rely on healthy Highland river systems.[6]

 

What is the future level of risk?

By the end of the century, the risks to freshwater ecosystems in the Highland region are projected to intensify significantly as climate change alters temperature, precipitation, and hydrological patterns. Modelled scenarios indicate that mean annual air temperatures in the Highland region could rise by up to 4°C by the 2080s, with warmer, drier summers and wetter winters. These changes will drive higher river and loch temperatures, exacerbating thermal stress for cold-water fish species such as Atlantic salmon, brown trout, and Arctic charr, and shifting species distributions northwards and upstream.

Episodes of prolonged low flow and drought are likely to become more frequent and severe, increasing deoxygenation, concentrating pollutants, and reducing connectivity between habitats.[7] By the 2050s, water temperatures in Highland lochs are projected to rise by around 3°C, pushing many systems above critical thresholds for algal bloom formation for one to two months each year, greatly increasing risks to ecological health and water supply quality. Longer and more intense stratification, combined with altered rainfall and reduced flushing rates, will further amplify nutrient release, deoxygenation, and ecosystem disruption across both shallow and deep lochs in the region.[8]

More intense rainfall events will increase flood frequency, accelerate sediment mobilisation, and erode fragile upland soils, particularly where riparian woodland is sparse.[9] Hydrological instability will damage spawning gravels, smother benthic habitats, and reduce water clarity. Warmer, nutrient-enriched conditions will further favour algal blooms and invasive species such as North American signal crayfish and non-native aquatic plants. The combined effects of rising temperatures, altered flow regimes, and biological invasions are expected to push many Highland freshwater systems beyond ecological thresholds, reducing their resilience, biodiversity, and capacity to deliver key ecosystem services such as clean water provision, carbon storage, and natural flood management.

 

Is the risk being managed or adapted to?

Adaptation and management efforts for freshwater ecosystems in the Highland region are progressing but remain uneven and constrained by resources and institutional capacity. Regulatory frameworks led by SEPA and the Scottish Government provide a strong foundation through the River Basin Management Plan for Scotland 2021–2027, which sets a target for 81% of the water environment to achieve good or better condition by 2027.[10] Actions under this plan include improving riparian habitat, tackling diffuse pollution, and restoring natural hydro-morphology through programmes such as the Water Environment Fund and Rural Diffuse Pollution Management Initiative. These measures have delivered local improvements but are yet to match the scale of projected climate pressures, particularly in upland catchments prone to drought and high temperatures.

Riparian woodland restoration, led by organisations such as the Riverwoods Initiative and local fisheries trusts, is enhancing shade and habitat complexity along Highland rivers.[11] Projects such as Pearls in Peril demonstrate integrated catchment-scale interventions that deliver co-benefits for biodiversity, flood regulation, and water quality.[12] However, gaps remain in monitoring, data coverage, and coordination between land-use and freshwater policies.

Highland Council’s Ecology Strategy and Action Plan (2024) emphasises safeguarding water quality, managing invasive species, and protecting wetlands, but local implementation depends heavily on continued funding.[13] Without sustained investment, widespread riparian reforestation, and enhanced management of water abstraction, existing actions will be insufficient to prevent climate-driven degradation of freshwater ecosystems across the region.

 

Are there benefits from further action in the next five years, over and above what is already planned?

Further action in the next five years offers the opportunity to strengthen the resilience of Highland freshwater ecosystems. Expanding riparian woodland creation is among the most effective measures available. The Riverwoods for Scotland – Report on Scientific Evidence (2022) highlights that extensive riparian planting provides multiple climate adaptation benefits, including localised cooling of river temperatures, reduced sediment and nutrient runoff, stabilised banks, and improved habitat connectivity. Targeted delivery across key Highland catchments including the Spey, Ness, and Oykel could rapidly enhance ecological resilience while supporting flood mitigation and carbon sequestration.[14]

Investment in integrated catchment management would also yield substantial gains. Strengthening collaboration between SEPA, the Highland Council, and land managers to align land use, water abstraction, and flood risk planning could reduce diffuse pollution and better regulate flows during drought and storm periods. Expanding monitoring networks, such as the Scotland River Temperature Monitoring Network, and implementing early warning systems for algal blooms would improve adaptive management and safeguard drinking-water supplies.

Accelerating implementation of Nature Networks and wetland restoration under the Scottish Biodiversity Strategy to 2045 – Tackling the Nature Emergency in Scotland could further strengthen ecological connectivity, aiding species migration and recovery.[15] Prompt action now would also reduce future restoration costs, prevent the loss of ecosystem services, and contribute to community and economic resilience by improving water quality, biodiversity, and recreational value.

 

Cascading and Interacting Risks

Risks to freshwater ecosystems in the Highland region are closely interlinked with wider climatic, ecological, and socio-economic systems, creating cascading and interacting effects across multiple sectors. Higher air and water temperatures, for example, reduce dissolved oxygen levels, which in turn heighten fish mortality and weaken populations of key species including salmon. Declining fish populations affect tourism and local economies reliant on angling and river-based recreation. At the same time, warmer, drier summers lead to greater water abstraction for agriculture and private supplies, amplifying low-flow stress in rivers and lochs and further concentrating pollutants.[16]^,[17]

Increased winter rainfall and flooding can mobilise sediment, nutrients, and pathogens from degraded upland soils, exacerbating eutrophication and reducing water quality downstream. These processes interact with the spread of invasive species such as North American signal crayfish, whose impacts intensify in warmer, nutrient-enriched waters. Catchment degradation also weakens natural flood defences, linking freshwater decline to heightened flood risks for settlements, transport routes, and critical infrastructure.[18] Such interdependencies mean that deterioration in freshwater condition can trigger wider ecological imbalance, economic loss, public health risks, and reduced resilience across Highland landscapes, underlining the need for integrated adaptation and land-water management.

 

Options for regional collaboration

• Expand catchment-scale restoration through coordinated riparian woodland networks, prioritising upper catchments of major river systems such as the Spey, Oykel, and Ness to reduce thermal stress, stabilise banks, and improve biodiversity connectivity.
• Develop a Highland-wide freshwater monitoring and early warning network, building on the Scotland River Temperature Monitoring Network to include real-time tracking of drought, algal blooms, and water quality hazards.

Resources

[1] Cosgrove, P., Shields, D., Anderson, D. and Massey, K. 2021. Understanding the impact of the 2018 drought on key freshwater pearl mussel populations in Scotland. NatureScot Research Report No. 1210.

[2] Kirkpatrick Baird, F., Stubbs Partridge, J. & Spray, D. 2021. Anticipating and mitigating projected climate-driven increases in extreme drought in Scotland, 2021-2040. NatureScot Research Report No. 1228.

[3] Linda May et al. (2022). Assessing climate change impacts on the water quality of Scottish standing waters. CRW2020_01. Scotland’s Centre of Expertise for Waters (CREW). Available at: www.crew.ac.uk/publications

[4] Linda May, Philip Taylor, Iain D. M. Gunn, Stephen J. Thackeray, Laurence R. Carvalho, Peter Hunter, Mairéad Corr, Anne J. Dobel, Alanna Grant, Gemma Nash, Emma Robinson and Bryan M. Spears (2022). Assessing climate change impacts on the water quality of Scottish standing waters. CRW2020_01. Scotland’s Centre of Expertise for Waters (CREW). Available online at: www.crew.ac.uk/publications

[5] Scottish Environment Protection Agency, “The River Basin Management Plan for Scotland 2021 – 2027” (SEPA, December 2021), https://www.sepa.org.uk/environment/water/river-basin-management-planning/.

[6] Hunt, A., England, K. and Watkiss, P. (2024). An economic assessment of climate risks and opportunities for the Highland Food and Drink sector. In: Highland Climate Risk & Opportunity Assessment.

[7] Linda May, Philip Taylor, Iain D. M. Gunn, Stephen J. Thackeray, Laurence R. Carvalho, Peter Hunter, Mairéad Corr, Anne J. Dobel, Alanna Grant, Gemma Nash, Emma Robinson and Bryan M. Spears (2022). Assessing climate change impacts on the water quality of Scottish standing waters. CRW2020_01. Scotland’s Centre of Expertise for Waters (CREW). Available online at: www.crew.ac.uk/publications

[8] Linda May et al. (2022). Assessing climate change impacts on the water quality of Scottish standing waters. CRW2020_01. Scotland’s Centre of Expertise for Waters (CREW). Available at: www.crew.ac.uk/publications

[9] Scottish Environment Protection Agency, “The River Basin Management Plan for Scotland 2021 – 2027” (SEPA, December 2021), https://www.sepa.org.uk/environment/water/river-basin-management-planning/.

[10] Scottish Environment Protection Agency, “The River Basin Management Plan for Scotland 2021 – 2027” (SEPA, December 2021), https://www.sepa.org.uk/environment/water/river-basin-management-planning/.

[11] Riverwoods for Scotland – Report on Scientific Evidence, 2022, Riverwoods Evidence Review | Riverwoods

[12] Environment and Forestry Directorate, Scottish Government, “Scottish Biodiversity Strategy to 2045” (The Scottish Government, November 27, 2024), https://www.gov.scot/publications/scottish-biodiversity-strategy-2045/.

[13] The Highland Council, “Ecology and Strategy Action Plan” (The Highland Council, November 2024), https://www.highland.gov.uk/info/1210/environment.

[14] Riverwoods for Scotland – Report on Scientific Evidence, 2022, Riverwoods Evidence Review | Riverwoods

[15] Environment and Forestry Directorate, Scottish Government, “Scottish Biodiversity Strategy to 2045” (The Scottish Government, November 27, 2024), https://www.gov.scot/publications/scottish-biodiversity-strategy-2045/.

[16] Scottish Environment Protection Agency, “The River Basin Management Plan for Scotland 2021 – 2027” (SEPA, December 2021), https://www.sepa.org.uk/environment/water/river-basin-management-planning/.

[17] Hunt, A., England, K. and Watkiss, P. (2024). An economic assessment of climate risks and opportunities for the Highland Food and Drink sector. In: Highland Climate Risk & Opportunity Assessment.

[18] Riverwoods for Scotland – Report on Scientific Evidence, 2022, https://www.riverwoods.org.uk/resource/riverwoods-evidence-review/ 

Key Definitions

For the HCCROA, the terms risk and opportunity are used in specific ways. Risk refers to the potential for climate change to cause harm to people, nature, buildings, infrastructure, and communities. Opportunity refers to the potential for climate change to alter conditions in ways that could be advantageous for certain activities, sectors, or places in the Highland region, relative to current conditions. These opportunities may arise alongside significant risks and do not offset or negate them.

The assessment also highlights a second kind of opportunity: opportunities for action. The HCCROA refers to options for regional collaboration, which are distinct from opportunities arising directly from climate change. Greater benefits may be realised from coordinated action to reduce risks than from relying on limited advantages associated with changing climate conditions themselves.

 

Mental Health

Climate change is a difficult topic to engage with, and Highland Adapts appreciates that this report presents potentially upsetting information. Visit the Highland Mental Wellbeing website to learn about mental health services, information, and training available in the Highland region.

 

Project Funding and Disclaimers

Core Highland Adapts funding is provided by its partner organisations. The HCCROA was partially funded by the Scottish Government’s Climate Ready Regions Grant. The views expressed in this document are not necessarily those of the Scottish Government. Its members, servants or agents accept no liability whatsoever for any loss or damage arising from the interpretation or use of the information, or reliance upon views contained herein.

The HCCROA is a product of the Highland Adapts partnership, conducted with support from Joseph Perry Consulting, Highland Adapts partner organisations, and other regional and national contributors. The analysis, findings, and conclusions presented in the HCCROA do not necessarily reflect the views of Highland Adapts partner organisations. The HCCROA is provided for general information and should not be regarded as a substitute for professional or technical advice. Highland Adapts, Joseph Perry Consulting, the report authors, and report contributors accept no responsibility for any loss or damage arising from the use or interpretation of information contained within the HCCROA.

This page was last updated on 2 Mar, 2026.