Few creatures better embody the nature of urban wildlife in Esther Woolfson's "hidden city", Aberdeen, than the herring gull. Its "profound, plaintive" cries echoing along the laneways of Old Aberdeen, it strikes many as an interloping pest, yet in its native coastal habitat, it is in worrying decline. It has a reputation for aggression, but is monogamous and lives amicably alongside its neighbours over a lifespan of up to 30 years. Move to Aberdeen, as I did recently, and you will assume the herring gull is as Aberdonian as granite and haar. Yet larus argentatus only moved inland from the seafront in the last century.

Similarly, oystercatchers are not the kind of bird you expect to see on a suburban grass verge, but Aberdeen has the largest number of roof-nesting oystercatchers in Europe. The Gaelic for this attractive wader is gille-brighde, St Bridget's servant, and legend has them helping Christ to hide from his enemies under some seaweed on a visit to Scotland. The shift from quotidian sightings to the hinterlands of mythic lore is typical of Field Notes, which promises a suburban focus only to fly its coop repeatedly; though getting outdoors at all is new territory  Woolfson's last book, Corvus, was an account of her home life with a host of rescue birds, chiefly a crow called Spike.

Just like the herring gull a century ago, contemporary nature writing is migrating into cities, albeit with publishing trends as much as evolution forcing the pace. Field Notes takes the form of a year's worth of diary entries, starting in the depths of winter. A cliché about Aberdeen is that it is the sunniest city in Britain, the only catch being that much of this sun is to be had at four in the morning. Woolfson is not to be discouraged, however, and is often awake in the small hours in search of the elusive aurora borealis. With or without the northern lights there is always something to inspect in the back garden or along the nearby river Dee, from rats and squirrels to a dead shrew. Plants get a look-in too, but much of Woolfson's gardening policy, she announces, comes down to the Chinese principle of wu wei, or "masterly inactivity".

These field notes provide springboards to wider meditations on our attitudes to the natural world. Distress at our unthinking cruelty runs through Woolfson's text. Lab rats have been shown to display empathetic behaviour, but Woolfson is more interested in what drives humans to speculate about how traumatising rats might find it when forced to witness other rats being decapitated. The sadism is not a side-effect, she realises, but the point and purpose of much of our treatment of animals.

The 17th-century Jesuit Guillaume-Hyacinthe Bougeant found a literally devilish rationale for animal abuse in his Amusement philosophique sur le langage des bêtes, arguing that, while animals lack souls, as empty vessels they form ideal hiding places for demons. It is therefore not just permissible but commendable to treat them violently.

Woolfson's Aberdeen golfer who clubs a fox to death would evidently agree, as would the writer of letters to a local paper each spring boasting of her trapping and killing of "cruel" magpies. By contrast, ascetic Jainists use muslin bags to filter their water for small waterborne insects and avoid potatoes and root vegetables, because of the harm done to earth-dwelling creatures in harvesting them. Yet after a loving description of rats she has known, Woolfson finds herself dealing with a rodent infestation and forced to call in the pest exterminators. "I accept that we live in a world of contradictions," she writes, "although it makes me feel no better."

Another contradiction emerges from a discussion of the red squirrel, which clings on in Scotland in the face of strong competition from its parvenu grey cousin. A local wildlife organisation in Aberdeen will supply traps for greys, and once they are caught, it will come and "dispatch" them. Woolfson bridles at the insistence on our "affinity" with the lovable red over the invasive grey, especially given the apparent absence of reds in Scotland before the 15th century and the murderous activities of the "Highland Squirrel Club", which got through tens of thousands of the creatures in the early 20th century. Affinity indeed.

I remember the flurry of indignant emails I received from a well-known poet for the crime of using the term "nature writing" without appropriate sarcasm, the term being infra dig for any self-respecting activist. Woolfson fills her text with poetry quotations, though her Catullus inexplicably comes out in prose and her disquisition on the passenger pigeon misses a trick in not referring to Mark Ford's fine elegy for that unfortunate bird. There is plenty of poetry in the beautiful descriptions of her garden and its hinterland, but while Woolfson specialises in bringing birds into her house, the suspicion remains that, when she herself takes wing, she will take the fight to the enemy with merciless force.

 David Wheatley's A Nest on the Waves is published by the Gallery Press.

There's a slow sea change taking place in how we view nature. Gradually, people are beginning to realise that cherishing the exotic and the rare is not necessarily the most helpful kind of conservation. Often, what we really need to do is learn to appreciate the local, the common and the unfavoured.

The same tendency is becoming apparent in nature writing too, that unlikely boom industry of the new millennium. From Paul Farley and Michael Symmons Roberts's Edgelands to Kathleen Jamie's Findings, from Jean Sprackland's Strands to the grandfather of them all, Richard Mabey's The Common Ground, writers are increasingly shifting their attention from virgin wilderness to the urbanised and polluted world we ordinarily inhabit, and to the kinds of species that live cheek by jowl with humans, so seemingly ubiquitous that most of us regard them as pests, assuming we bother to see them at all.

An example would be the magpie, that egg-stealing bandit of urban mythology. Back in 2008, Esther Woolfson published Corvus, a delightful ode to the maligned crow family, many of which she'd adopted over the years. She possessed a naturalist's loving attention to detail, combined with a likable fondness for demolishing superstitions. An ideal candidate, then, for a larger take on urban wildness, and why it's so important for our wellbeing, not to mention our continued survival.

In Field Notes, Woolfson turns her beady eye to the muddled and fascinating ecology of her hometown of Aberdeen. Her diary begins on a day of uncommon snowfall, the harbinger of a period in which the entire city shivers to a standstill. Finding a wounded pigeon flailing in the lane, she takes it home to nurse. The weather is off-kilter, and the bird "seemed to symbolise the fragility that suddenly I felt was there, at the heart of everything".

Over the course of a year, her sense that something has gone awry intensifies. It's too wet; the winter's untimely and summer barely lasts a week. Is this androgenic climate change, Woolfson wonders, and her growing anxiety infuses the book with a kind of hyper-attentive urgency, a desire to record exactly "the lives and time and place" among which she finds herself.

The Aberdeen she unearths is a beguiling city. Woolfson borrows a key to investigate an otherwise inaccessible strip of wilderness between two rows of houses, where a Victorian botanist once led his students on summer expeditions. Behind a chain-link fence, she discovers the largest quarry in Europe, out of which much of the granite for Aberdeen's houses derived. Abandoned in 1970, it filled with water to form a vast lake. "More than part of the city unseen, it seemed like the city's secret; a strange irony considering that it's where most of the city came from."

Though her hidden city extends back through time, it's the living inhabitants that capture the larger part of Woolfson's attention and enthusiasm. There's nothing mystical about her enthusiasm for spiders, worms, shrews and foxes, but rather a kind of bustling curiosity about their strange and purposeful lives. Some slugs, she reports gleefully, mate by way of what is known even in scientific papers as a "love dart", a small blade of chitin or cartilage that may have provided the Greeks with the inspiration for Eros's arrow. Rats, meanwhile, have been proved to refuse to take food if by doing so they cause pain to other rats, a sign suggestive that they, like us, experience empathy.

Little in the world of conservation is simple, and this is particularly true of the vexed subject of invasion biology. After spotting a red squirrel crossing a road at a traffic light, Woolfson begins to ponder the odd and often tortuous logic by which so-called native species are regarded as inherently superior to "invaders". One list of the world's worst invasive species includes foxes, rabbits, mice and pigeons. Even Himalayan balsam, that aggressive coloniser of riverbanks, seems potentially less lethal than was once imagined. "To which moment might we wish to retreat, pull up our drawbridge, erase from memory what we ourselves, or the processes of nature and time, have wrought?" she asks, pointing out, too, the uncomfortable rhetoric of nationalism and violence that often accompanies the debate.

Though Woolfson maintains a spirited sense of inquiry, the overwhelming mood here is of oncoming loss, and bafflement as to how we've managed to make such a poor fist of stewarding our inherited Eden. Writing on the subject of sparrows, those once abundant, now critically endangered residents of our cities, she writes movingly: "If we lose sparrows, everything will change. Our lives will change, even if we don't at the time fully appreciate how As with every loss, our lives will be thinner, lesser; the future not only of the physical but our mental world will be diminished, the world of our history and legend where the life of all cultures resonates with all we've seen and all we've lived with, plant and animal, stone and cloud."

She's right. It can only be hoped that books like this play a part in making us both notice and value the lovely creatures we stand to lose, before the wild portions of our cities have been entirely swept and tidied and paved out of existence.

Olivia Laing's To the River is published by Canongate (£7.99)