The river, which is designated both a Site of Special Scientific Interest (SSSI) and Special Area of Conservation (SAC), was assessed by Scottish Natural Heritage as part of a national study of the country’s protected areas.
The report found that just 35.7 per cent of the Tweed and its associated features were in ‘favourable’ condition. This compares to 77.2 per cent Scotland-wide.
A spokesperson for Scottish Natural Heritage explained why the Tweed was classed as being overall in an unfavourable condition.
She said: “It covers such a huge site, including tributaries of the Tweed, so when something detrimental happens in one area, it affects the whole area.
“The size of the site also means collaborative work is more complicated, with many land managers involved.”
She added: “Three species of lamprey are included and lower the stats for the Tweed - lamprey are rated unfavourable in about two-thirds of the sites where they’re present in Scotland.”
Nick Yonge, clerk to the River Tweed Commission, said he he knew nothing of the report or the methodology behind it and was not prepared to comment on it specifically.
Just last week, the Tweed Foundation’s senior biologist Dr Ronald Campbell reported on his blog that salmon fry had been found in the upper Leet for the first time.
He said: “This is the first time we’ve evidence of salmon spawning in the upper Leet, which has been the worst part of the catchment in terms of physical environment and water quality.”
Commenting on this significant discovery, Mr Yonge said: “The Leet has been very difficult for lots of reasons, and local people have been jumping up and down about it for a long time.”
He added: “Quite a lot of the Leet has been fenced off which then stops intensive grazing right up to the riverbank.
“This allows the undergrowth to overhang, which provides shade and shelter for fish and a lot of things living in the overhanging vegetation fall into the river and that provides food for the fish.”
Mr Yonge added: “It also provides a buffer and if there is fertiliser or manure put on the fields it acts almost like a sponge and stops run-off into the river.”
Just over 77 per cent of the natural features across the 1,881 protected sites assessed by Scottish Natural Heritage were rated as ‘favourable’.
However, the report stated that there was ‘no meaningful change’ in the proportion of features in favourable condition between 2010 and 2011, although since 2005 it had increased by almost six per cent.
Angus Laing, Scottish Natural Heritage’s protected places unit manager, said: “We are disappointed that there’s been no improvement this year, but changes to entire ecosystems have to be measured over decades, not years.
“Since 2005, the 5,478 protected habitats and species in Scotland have improved by more than six percent - this is no mean feat when you look at the range and area involved.
“But there’s no avoiding the fact that we now face even bigger challenges, which may mean the increases are more gradual in the coming years.
“Some of the early changes were obvious and easily made – now, we are involved in complex, joint management between a number of landowners.
“Dealing with invasive species is also difficult on many designated sites, without destroying the vegetation we’re trying to protect. Added to this, climate change may be affecting many of our habitats and species unpredictably.”
Mr Laing added: “But, we are working as hard as we can to improve the condition of Scotland’s protected natural areas. A huge amount of work has been carried out by public bodies, conservation organisations and private individuals and companies, and we all must continue to work together to reach the Scottish Government’s ambitious target of 95 percent in favourable condition and make sure Scotland’s nature thrives.”