Take your pick. UK conservation is in crisis, or it has never been in ruder health. Believe the government and English and Welsh rivers are the cleanest they have been in a century, fish are returning, protected areas are in fantastic condition and the air is clean.

Yet for others, the ecological health of the nation is worsening by the day as resources to protect nature and people are slashed, the forestry estate and national nature reserves are put up for sale and thousands of people who have spent lifetimes battling to protect Britain's most beautiful places and wildlife face redundancy.

The environment secretary, Caroline Spelman, is relentlessly upbeat, saying in a New Year's message that

more than 95% of England's finest wildlife and geological sites covering more than one million hectares of countryside is in "favourable or recovering" condition.

Beware the spin. Only in September, prof Sir John Lawton and a team of leading conservationists came to a very different conclusion than Spelman's about the state of Britain's SSSIs (Sites of Special Scientific Interest). According to their independent report, commissioned and welcomed by the government, just 30% of them were actually in favourable condition. The rest were "unfavourable recovering".

This what they actually said (emphasis mine):

When this report was being written in August 2010, the 95% target was in reach, with 93% of SSSIs now considered to be in favourable condition or under appropriate management and so qualifying as unfavourable recovering (although we note that 63% is currently in this latter category, while just 30% is assessed as actually favourable).

To gauge the true state of British conservation and wildlife, we must look at the government's own statistics, eked out every few years in reports to parliament and Europe, in sustainable development indicators and in independent reports. There, no amount of spinning can hide the fact that figures are being carefully picked, and that the government is not presenting the true picture.

Take biodiversity. Natural England, the government's statutory ecological advisers, admitted in 2009 that Britain was concentrating on oases of high environmental quality but ignoring the ecological deserts that surround them. This week, however, they were upbeat. Here is the CEO, Helen Phillips:

The turnaround in the fortunes of England's SSSIs is one of the great conservation success stories of recent decades and owes much to the tireless efforts of an army of conservationists, landowners and volunteers. Thanks to their efforts, a host of rare species, from sand lizards to golden plovers, now have a greater prospect of flourishing; while much-loved landscapes, such as the New Forest and the Yorkshire Dales, face a more secure future.

In fact, the latest available statistics show that the vast majority of the species and habitats identified by the government as being most in need of conservation action showed no improvement whatever between 1999 and 2008, while 125 species out of 289 actually declined in quality or extent.

"Of the 289 species for which an assessment was made in 2008, 88 were still declining and eight had been lost from the UK since the plan was published in 1994. Those that were stable may have populations well below target levels," said the report. "In 2008, an assessment was made of 35 habitats; 15 (44%) were still declining in extent."

Birds are faring terribly, too, despite Spelman's declaration that the apparently dramatic improvement in the state of Britain's SSSIs is helping them. According to its own statistics, the farmland bird population index fell 47% between 1970 and 2008 and by 23% between 1990 and 2008. In 2008, the woodland bird population index was actually 14% lower than in 1970, and 7% lower than in 1990.

Slightly more than two years ago, the last time the survey was conducted, the government said: "Of the 289 species for which an assessment was made in 2008, 88 were still declining and eight had been lost from the UK since 1994."

Equally, ministers give the impression that everything is just fine with our rivers, and that water quality is getting better by the day. Just 15 months ago, the Environment Agency could report that the quality of rivers in England and Wales was the best it has been for more than a century, and that otters, eels and salmon were set to return to the Thames and Mersey.

But these statements carefully ignore new European legal standards that show nearly 75% of all rivers in England and Wales fall well below the highest European environmental standards, with only 26% of rivers now classified as "good" quality, and only five rivers out of nearly 6,000 reaching the highest standards.

The reality is that 117 rivers are classified as being in "bad" condition, on a level with the most polluted in eastern Europe. A further 742 were in "poor" condition and 3,654 (60%) were "moderate".

Lakes are seldom mentioned by the government, but are in a lousy state as well. Only one out of 762 lakes in England and Wales is considered by Europe to be of "high" status. Seven are considered "bad" – meaning they are close to being biologically dead. A full 70% are officially in line to miss the targets set for them by Europe.

But the government continually spins the figures. In response to the European water quality directive, the CEO of the Environment Agency, Paul Leinster, said: "Our rivers are at their cleanest for over a century, which is why we are seeing the return of otters, eels and salmon to the Thames, Mersey and Tyne."

He was technically correct, but it was only a small part of the wider truth. "It's very misleading about the state of freshwater generally," says Jeremy Biggs, head of conservation charity Pond Conservation. "Streams and rivers make up about one third of the water environment; the rest is ponds and lakes. Ponds and lakes have probably never been worse, even though the agency is supposed to look out for all freshwaters."

What ministers mean, Biggs says, is that the dirtiest river estuaries where big cities such as London and Liverpool discharge into a big river are indeed much cleaner, and some of the worst pollution in the industrial Midlands and north has gone. "But no account is taken of what has happened to rivers in between, in what were once rural areas, and how much of that has declined. In rural Wales, there's now less high-quality river length than in 1990."

The Thames is always held up to be in tip-top condition, and recently won an international award for its restoration, but the reality is very different, says Biggs, who makes a distinction between the river itself and areas in its catchment.

"In fact, while the chemical water quality has improved a bit in rivers across the Thames area, the biological river quality – which is really what we're all interested in – is actually worse than in 1995," he says. "The length of river in 'good' biological condition in the Thames catchment area is now lower than in 1995." In the Thames area, where there is a 140-year continuous monitoring record of nitrates just west of London, levels are higher than in Dickensian times, he says.

The government is spinning the fish statistics equally hard. Salmon in the Tyne are widely used as an example of general improvement across England and Wales, when in fact the opposite is true. Nationally, the records show salmon stocks have never been lower, and in 2009 were the lowest since records began.

To listen to the government, you would barely know that other freshwater species were in rapid decline. According to the Environment Agency's website, sea trout are faring especially badly. It says: "Sea trout stocks appear to have been declining in recent years, with the declared rod catch in 2007 (29,398) showing a decrease of 25% compared with the mean of the previous five years (39,117), although care should be taken when relating catch to run size."

What government agencies and ministers are doing is continually overemphasising the positive, cherry-picking a few success stories to blind us to the real state of the environment and deliberately ignoring broader indicators that use wider and more sophisticated ranges of measures of quality. It's politically convenient, but misleading, and serves neither the environment nor people well.