Listen: on this chilly afternoon at the end of March, Blean Woods are reverberating with birdsong. Several robins are uttering the twittering warbles that proclaim their territory, a chiffchaff is slipping out its metronomic, two-note call, and every couple of minutes a green woodpecker fires off its yaffle – its staccato burst of notes carries through the trees. Over it all a song thrush is singing from the top of a still-leafless chestnut, silhouetted against the sky; it is enormously loud for such a squib of a thing, each phrase repeated with such cold sweet clarity that it triggers in the mind Philip Larkin's memorable catching of just such a bird, singing in a garden at just this time of year: "its fresh-peeled voice/ astonishing the brickwork".

Good place for birds, then, Blean. The woods stretch for miles over the rolling hilly ground to the north-west of Canterbury, one of the largest continuous blocks of ancient broadleaved woodland in southern England; in fact they're second only to the New Forest in their extent. For more than a thousand years they were owned by various ecclesiastical establishments in Canterbury; now the part where I am standing constitutes Blean Woods National Nature Reserve, owned and managed by the Royal Society for the Protection of Birds (RSPB), in partnership with Natural England, the Woodland Trust, and three local councils.

I am talking to Michael Walter, who has been the RSPB warden, continuously, since his society took over the woodland in 1982, and as might be expected, we are talking birds. You can see a lot in Blean: the woods hold all three native British woodpeckers, nuthatches and tree creepers, several warbler species, good numbers of nightingales and solid populations of the commoner birds such as wrens, robins, tits and thrushes. But we aren't talking about what's here. We're talking about what's not here any more.

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In the quarter-century since Michael Walter came to look after Blean Woods, they have suffered a remarkable series of declines in their breeding bird species. Eight have become extinct altogether, birds that were nesting in the woods when he arrived, and have now vanished. He enumerates them: cuckoo, redstart, wood warbler, golden oriole, hawfinch, willow tit, yellowhammer and starling. Seven more species have suffered severe declines: turtle dove, tree pipit, spotted flycatcher, whitethroat, marsh tit, nuthatch and jackdaw (some of them barely clinging on). This has happened despite the fact that the warden is an expert on actively managing woods for birds, and has spent 25 years striving to make Blean as ideal an avian habitat as it could possibly be.

But Michael Walter's experience is not unique. It is a reflection of a disquieting development taking place over much of Britain: the decline of our woodland birds. In recent years ornithologists have recognised that a dozen or so largely woodland species are plunging in numbers, to the point where the graphs of their decline slope down sharply towards extinction.

We are already aware of catastrophic declines in one section of our avifauna: the birds of farmland. Starting somewhere about 1960, familiar species that once enlivened every country walk, such as the grey partridge, the skylark, the lapwing and the yellowhammer, began to fall in numbers and then disappear, to the point where nowadays there are whole regions where they can no longer be encountered. They made a desert, and they called it farming. In 30 years, the corn bunting – a fat finch with a song like a jangled bunch of keys – declined by 87 per cent. Our native grey partridge went down by 86 per cent (the partridge you will see in most of Britain now is its cousin, the red-legged or French version). The starling – common as muck, used to be everywhere – declined by 80 per cent. The turtle dove declined by 77 per cent, the linnet by 68 per cent, the skylark by 60 per cent, and so it went on.

This unpardonable impoverishment of our natural world has become a major concern; reversing these declines is now an official Government objective. Yet there is one consolation: there is a single cause, which is known. Agricultural intensification. When modern farming methods replaced the age-old ways of doing things, they impacted direly on birds that were dependent upon the practice of agriculture. As new techniques were brought in – the planting of winter as well as summer crops with consequent loss of autumn stubble fields, the replacement of hay with silage, the switch from old meadows to modern grasslands, the drenching of fields in pesticides and let's not forget the manic, mass tearing-out of hedges in the absurd years of overproduction under the European Union's Common Agricultural Policy – the niches, the living spaces where farmland birds were able to feed and breed, disappeared.

Yet at least the reason was apparent, so remedial action could be taken (in the form of stewardship schemes under which farmers are paid to recreate the older wildlife habitats). With woodland birds, it is different. There is no one obvious explanation for the disappearances. Instead there are several factors that seem to have come into play at the same time, and so affected a wide range of species. Furthermore, the woodland declines were less obvious, for you know when you don't hear skylarks any more on your walk across the fields, but when hawfinches vanish from the leafy canopy of your wood, you may not have known that these handsome but secretive songbirds were there in the first place.

Yet about the time of the Millennium they began to be picked up, and the British Trust for Ornithology (BTO), the UK's leading scientific bird research organisation, decided to examine them in detail. Its study reported in 2003 with surprising results. Over the previous 35 years, there appeared to have been declines of greater than 50 per cent in 10 woodland bird species, which in order of magnitude were: spotted flycatcher, lesser spotted woodpecker, lesser whitethroat, lesser redpoll, tree pipit, willow tit, marsh tit, woodcock, dunnock and willow warbler. Other sources of information suggested there had been significant losses in a further group of species, including hawfinch, wood warbler, and nightingale.

The BTO then decided to have an even closer look at what was happening, and joined forces with the RSPB for a large-scale investigation: the Repeat Woodland Bird Survey (RWBS). This looked again at 406 woods that between them the two bodies had surveyed 20 years earlier, and in 2006 came up with its own picture, confirming much of the first study, but adjusting its findings in what was probably a more accurate way. The top 10 declines the RWBS registered, in its own order of magnitude, were: tree pipit, hawfinch, willow tit, willow warbler, lesser spotted woodpecker, lesser redpoll, wood warbler, redstart, garden warbler and spotted flycatcher.

Some of these are among the most appealing creatures on God's earth. Take the two that are labelled spotted, the spotted flycatcher and the lesser spotted woodpecker. (Neither is all that spotted.) The first is about as sober in its colour scheme as it is possible to be, plain grey-brown above and pale below, but there is a harmony in its shape, a restrained elegance in its upright pose, that is quite captivating. The second is a woodpecker in miniature, with all a woodpecker's charismatic liveliness and colour – black, white and scarlet like its great spotted cousin, increasingly familiar on garden bird tables – yet this thing is the size of a mobile phone, and so elusive that just catching sight of one feels like a triumph. All these birds, in fact, have their own charm: the willow warbler's descending fall of song is one of the emblematic sounds of spring (seep-seep sip-sip sep-sep sop-sop sup-sip); its cousin the wood warbler, green and lemon-yellow, shivers its whole body when it sings; the hawfinch, hunky, bull-necked and pinkish-brown, would be the nearest thing we have in Britain to a parrot if we didn't now have the ring-necked parakeet; and the redstart, with its plumage of orange, slate-blue, black and white, is the most exotic decoration you're likely to see on a British fir tree short of Christmas. And we're losing them. Why?

To take the most direct possibility: is it predation? Might other creatures be killing them off? The answer is, perhaps – in some cases. Grey squirrels are the likeliest candidates; their populations in Britain continue to soar, and in their native American homeland they are major predators of birds' nests. The trouble is, there is little direct evidence, although the nest of a hawfinch on a branch in a wood canopy is in exactly the sort of place where a grey squirrel would encounter it. More outlandish candidates are great spotted woodpeckers, which have shot up in numbers enormously; they are known to predate upon their lesser spotted cousins, killing and eating the chicks in the nest. Conventional predators, such as sparrowhawks, crows and magpies, are all doing well, but again, there is simply no evidence that they are affecting whole populations.

A subtler thought is this. Has something gone wrong with the woods themselves? The answer is, more likely. Successful living space for several bird species in British woods has long depended on a traditional type of woodland management, many hundreds, if not thousands of years, old: coppicing. This means cutting trees down to ground level, and then letting new shoots grow back up from the resultant stumps, or stools. Coppicing provides a steady supply of long straight wood poles, traditionally used in fence making and for firewood, but for birds, it also provides, in its early stages, a dense shrubby layer, similar to the garrigue, the aromatic bushy landscape of Mediterranean countries, which is perfect for species such as nightingales and warblers to nest in.

From about the middle of the 20th century, however, coppicing began to be abandoned. When that happens, the shrub layer disappears; but not only that. When the trees grow up, eventually the canopy closes, shutting out the light; and the rest of the undergrowth, the brambles and bushes and plants that form the layer of ground flora, where other bird species love to forage and breed, dies off. Undoubtedly the abandoning of coppicing has played a part in woodland bird decline. And unfortunately, its negative effects are being strongly reinforced by another factor: deer. Virtually all species of deer in Britain are steadily increasing in numbers, led by the muntjac, a pint-sized Bambi introduced from China, whose speciality is breeding all year round. In many of Britain's woods, the browsing of deer is now so extensive that it is causing large-scale structural changes to the vegetation: in effect, Bambi and his pals are eating the undergrowth to bits.

This is definitely affecting bird populations. But why are deer booming? One reason: there is more food in the landscape, because crops are now in the fields all the year round. Another reason is probably climate change: winters are substantially warmer than 30 years ago, and many more young deer are surviving. Climate change = warmer winters = more deer = less undergrowth = fewer birds. It's a fairly long chain, although it looks a likely one. But climate change may also be acting directly on some woodland bird species. One candidate is the willow tit, a chunky, darker relative of the more familiar blue tits and great tits, which has suffered one of the worst declines. Over much of southern Britain, it has gone, or is going, extinct. It may be suffering from competition with blue and great tits which stock up on our garden feeders then go back into the woods to breed. But there is another possibility to do with the fact that the willow tit is the only tit which excavates its own nest hole. To do this it seems to need damp woods, but with rising temperatures, some woods which were once damp are now drying out.

Climate change may also be acting in a subtler way: creating a mismatch between the moment when abundant bird food appears in spring – in particular, lots of small caterpillars on oaks and other trees – and the moment when migratory birds wintering in Africa, arrive back in Britain to breed. The two used to occur together, but warmer springs mean oak leaves are sprouting earlier, and the caterpillars are emerging earlier with them; yet birds in Africa cannot see this happening, and come back at the same time as before, and so may be missing out on the abundance, and breeding less successfully. Research in the Netherlands indicates this is happening with pied flycatchers; it may well happen with other migrants.

Migrants, yes. There, perhaps is the most suggestive thought of all. If we look at all three lists of declining woodland birds mentioned above, in each case about half are long-distance migrant species that spend every winter in Africa south of the Sahara, and come back here to nest in the summer. There are seven of them in total: spotted flycatcher, wood warbler, tree pipit, redstart, willow warbler, garden warbler and golden oriole. All these woodland migrants are declining rapidly.

Picture them, tiny things, featherballs weighing a few grammes, which twice a year make journeys of thousands of miles across Europe, the Mediterranean, North Africa and then the world's harshest desert, facing hunger, thirst, heat, exhaustion, storms, predators and the seemingly impossible conundrum of navigation – often at night. In between, they wander the great continent for six months, seeking a living, seeking survival, and we know very little about where they go or what they do. It seems incredible that they can succeed in coming back, year after year, to woodlands in Norfolk and Dorset, in Wales and Scotland – so would it be so strange if, one day, they were to fail?

The decline in our woodland birds is thus alerting ornithologists to perhaps an even bigger problem – that the system of bird migration between Europe and Africa, millions of years old, may be running into trouble. Perhaps this too is climate change; perhaps it's habitat loss; nobody knows. A major research effort is just beginning, and the more scientists look, the more it seems that migrants are encountering difficulties, either on their epic journeys to and fro, or on their African wintering grounds.

What this means for somebody like Michael Walter at Blean Woods in Kent is that however hard he tries, there are some bird declines that he can do nothing about. And he has certainly tried hard. Over the past 25 years – he's 59 now – he has managed the coppicing of the woods so well that he still has good numbers of nightingales, willow warblers and garden warblers, all migrants that are plunging in numbers over much of England. But his wood warblers have gone, his golden orioles have gone, and his redstarts have gone; his turtle doves have collapsed in numbers, as have his spotted flycatchers, his tree pipits are hanging on by their clawtips (a single pair bred last year) and in 2007, for the first time in his quarter century as their custodian, Michael Walter did not record a single cuckoo in Blean Woods.

"The fact that I was coppicing intensively would have led me to believe that some of these species would at least have held their own, but instead, the declines here are just mirroring what's happening on a national scale, and that is certainly frustrating," he said. "What's the point in slugging our guts out doing the coppicing if we're not going to benefit all these species? What's the point of having a reserve, if all these lovely birds are going to disappear?"

He agrees that the causes are complex, but the phenomenon is real. "It would be an enormous coincidence for so many species to disappear or go down at the same time, so there is something at work, or a range of somethings. But we're still at the stage of proposing causes, and trying to establish whether they are related or not."

He certainly feels it, personally. Especially with the disappearing cuckoo.

"A bird like a cuckoo is emblematic, a symbol of spring. When you stop hearing them, you really do feel that something's gone desperately wrong."

To find out more visit rspb.org.uk