The study from the Scottish Government, pulling together key data from various environmental agencies, points to a decline in certain species, which can be attributed at least in part to the changing environment. It shows the sea bird population is dropping at an alarming rate - with some species shrinking by 95 per cent - although numbers of terrestrial breeding birds and wintering water birds are burgeoning.
And it highlights the worrying state of designated Sites of Special Scientific Interest - with almost half declining, destroyed or in an unfavourable condition.
Scottish Natural Heritage (SNH), which collated most of the data for Scotland's Biodiversity Indicators, by studying a broad range of 22 species and habitats, said while it contained areas of concern, it showed - through the monitoring of otters - there had been major improvements to waterways in the central belt.
According to one of the indicators, the mammals occupied 92 per cent of sites in 2004, up from 57 per cent in 1979.
Edward Mackey, of SNH, said: "Otters are a very good news story and very striking evidence that the damaged rivers of the central belt have been brought back into good ecological conditions. Otters are dependent on good-quality waters. Historically, they have been absent from the central Lowlands of Scotland because the Forth and Clyde were very heavily polluted in the past."
He said the same was true of the rivers' estuaries, which now held fish species that had not been there a few years ago - but not of the sea.
"We are well aware of reports of over-fishing and fish stocks - particularly cod - being fished beyond their capacity to recover. Fish stocks are quite sensitive to management, and of 11 stocks that were assessed only seven were at full reproductive capacity in 2005," said Mr Mackey.
He said another factor in the decline could be climate change, demonstrated by the indicator on plankton. Plankton which was suited to warmer seas was thriving, despite seas around Scotland being historically cold.
"We may be seeing a gradual shift in the marine environment," he said. "We can see it on land as well, in butterflies which are very responsive to weather conditions and climate. We are beginning to see the species which have increased are those generalised species that are very mobile. Conversely, there seems to be a decline in those restricted in their ecological requirements."
Mr Mackey said there was good news on the endangered species and habitats fronts - with 11 and six respectively now increasing - which suggested targeted action could work.
The bird charity RSPB Scotland also warned of the dangers of climate change shown in the indicators, and pointed to the drastic drop in breeding sea birds, including a 95 per cent drop in Arctic tern.
Its head of conservation policy, Lloyd Austin, said: "Although seabird problems are, at least in part, a symptom of climate change, they are, and will continue to be, exacerbated by unsustainable fisheries management and poor marine planning."
He called for legislation to protect the marine network and for a government commitment to sustainable fisheries.
The document was published as the UK Biodiversity Partnership Conference began in Aviemore.
Opening the event, the environment minister Mike Russell said Scotland should be "deeply proud" of its environment, but warned the report showed there were "major challenges" ahead.
He said: "Over generations humans have destroyed habitat, used resources unsustainably, introduced invasive species, and failed to protect wildlife. We are determined to reverse that damage wherever we can."
WHAT'S THRIVING ...AND WHAT'S THREATENED
AMONG the species studied in Scotland's Biodiversity Indicators, the otter has seen the most marked increase throughout the country.
The mammals rely on good-quality fresh water and had vanished from the Lowlands. However, they are back and experts say this is confirmation of improved environ-mental conditions and ecological quality.
Occupied sites rose from 57 per cent of Scotland in 1979 to 92 per cent in 2004.
The largest increases were in Forth and Borders (17 per cent in 1979 to 87 per cent in 2004) and Strathclyde and Ayrshire (24 per cent to 83 per cent). There were also increases in East Highland, Grampian, Argyll and Stirling and Tayside and Clackmannanshire.
Northern Isles, Western Isles, north Highland, west Highland and Dumfries and Galloway are thought to be close to their maximum capacity, at 96 per cent occupancy.
However, the research also shows a dramatic drop in breeding sea bird numbers, which can be studied to assess changes in the marine environment.
Between 1992 and 2004, numbers dropped by 30 per cent, compared to 1986 when monitoring started.
The overall decline is accounted for largely by drops in the Arctic tern, Arctic skua and black-legged kittiwake.
Overall, six species decreased - Arctic tern by 95 per cent - and seven increased.
Among them was the northern gannet which went up by 85 per cent.
Conversely, water bird numbers were shown to have increased by 27 per cent since 1975.
Research examined 37 different species and found sustained increases in many, including little grebe, Eurasian wigeon, gadwall, Eurasian teal, common eider, Eurasian oystercatcher and ringed plover.
There were declines in species including the mallard, common pochard and greater scaup.
Terrestrial breeding birds also fared well, with the 68 species studied increasing in abundance by 17 per cent between 1994 and 2004.
Woodland birds increased by 30 per cent and farmland birds by 10 per cent, while the trend for 16 upland birds was stable overall.
The butterfly population suffered mixed fortunes.
Overall, they were up by 35 per cent between 1979 and 2005. Species that increased included the red admiral, and the ringlet.
Declining species included the grayling and the dark green fritillary.