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One particular concern is the risk of more extensive algal blooms occurring.
Extensive algal blooms in Scotland have previously killed thousands of farmed salmon, with the algae sticking to the fish’s gills and suffocating them.
Toxic blue-green algae can also pose health risks to humans and can be deadly to pets like dogs.
The new research, by the UK Centre for Ecology & Hydrology, reveals that 97 per cent of the Scottish lochs and reservoirs they monitored increased in temperature between 2015 and 2019.
While most of these standing waters (88 per cent) warmed by 0.25C to 1C per year over this period, 9 per cent increased by more than that – some by up to 1.3C per year – a considerable rise.
The research team said that with water warming at this high rate, a projected increase in air temperature of 2.5C in Scotland between 2020 and 2080 would result in a 3C rise in lochs and reservoirs over that period.
This level of warming along with changes in rainfall patterns driven by the climate crisis increase the risk of outbreaks of harmful algal blooms.
This would restrict the use of Scottish lochs and reservoirs for recreation and water supply, and as a safe habitat for wildlife.
Freshwater ecologist Dr Linda May of UKCEH, lead author of the report, said: “This research has shown, for the first time, that climate change is already warming our lochs and reservoirs in Scotland, and that this trend is likely to continue.
“It provides early warning of the potential impacts of climate change on biodiversity, water supply and recreational use, and highlights the need for mitigation measures to be put in place as quickly as possible.”
The report also makes a number of recommendations including reducing the amount of phosphorus and nitrogen entering lochs and reservoirs from their catchments, because these are the other main driver of algal blooms.
These nutrients are present in synthetic fertilisers as well as human and animal waste, and sources of pollution in lochs and reservoirs include farm runoff and wastewater discharges.
Mairi McAllan, environment minister in the Scottish government, said the report would be “hugely valuable” in informing climate policy decisions.
She said: “This important research provides yet more worrying evidence of the risks of harm from climate change on Scotland’s water environment. It is vital that we do more to mitigate those impacts, to seek to reduce the pace of warming but also to adapt to it.”
The research was commissioned by Scotland’s Centre of Expertise for Waters.