the species staging something of a comeback with the help of reintroductions, conservation action and steps such as banning pesticides that were harming them.
But many of the successes have only brought numbers back to a fraction of their historic levels, the report warned.
And more than three-quarters (77%) of 155 species of birds, animals, butterflies and moths which are considered a priority for conservation action, including some of the country's rarest and most vulnerable wildlife, have seen declines in the last 40 years.
Species which rely on particular habitats have fared worse, and the declines in wildlife come against a background of massive loss of natural habitats in the past two centuries.
Four-fifths of lowland heathland has vanished since 1800, with falls in the range of species such as nightjars and ladybird spiders which rely on them.
Lowland meadows in England and Wales declined by 97% between the 1930s and 1984, while 90% of coppiced woodland vanished between 1900 and 1970, hitting a variety of plants and insects.
Almost half of Scotland's blanket bog (44%) was lost to forest plantation and drainage in four decades after the Second World War.
The collaboration between scientists and the conservation groups points to a number of causes for the declines, including loss of habitats, more intensive farming practices, invasive non-native species and illegal persecution of species, while there is mounting evidence of the harmful impacts of climate change.
But conservation work and recent moves such as creation of wetlands and improved water quality have helped nature.
Dr Mark Eaton, a lead author on the report, said: "This report reveals that the UK's nature is in trouble - overall we are losing wildlife at an alarming rate.
"These declines are happening across all countries and UK Overseas Territories, habitats and species groups, although it is probably greatest amongst insects, such as our moths, butterflies and beetles. Other once common species like the lesser spotted woodpecker, barbastelle bat and hedgehog are vanishing before our eyes.
"Reliable data on these species goes back just 50 years, at most, but we know that there has been a historical pattern of loss in the UK going back even further.
"Threats including sweeping habitat loss, changes to the way we manage our countryside, and the more recent impact of climate change, have had a major impact on our wildlife, and they are not going away."
The study's analysis of populations and range of 3,148 species dating back up to 50 years ago represents just 5% of the UK's estimated terrestrial and freshwater species, with many, particularly insects, plants and fungi, lacking sufficient data for assessment.
Some 6,225 species could be assessed under Red List criteria for their extinction risk and 755, or 12% were found to be under threat.