Philip Pullman is the living heir of Lewis Carroll and George MacDonald and, yes, CS Lewis – in spite of Lewis being his chief bugbear, whom he attacks furiously for his religiosity and misanthropy. While JK Rowling carried on the tradition of jolly school adventures and gripping supernatural yarns, he has chosen the pilgrim road of fantastic metaphysical allegory, and his new book nods to Spenser’s The Faerie Queene in the same way as His Dark Materials took on Milton and Paradise Lost. In this longed-for opening volume of the new trilogy, Pullman faces his lineage without apology: his young heroine is even called Alice, and the story follows her as she is swept down the Thames in the eponymous canoe of the hero, Malcolm. But whereas the Thames offered Carroll’s Alice an idyllic, pastoral meander, a very contemporary apocalypse explodes around this older Alice.

To begin with, La Belle Sauvage feels old-fashioned and comfy, set in a picture-book Oxford redolent of stewed cabbage, meat pies and generous helpings of pudding, lit by naphtha lamps and warmed by brandwijn. The action takes place 10 years before Northern Lights, and unfolds how Lyra, the once and future heroine of His Dark Materials, will come to grow up in the Oxford college called Jordan. The hero, Malcolm, a red-haired, good-natured, savvy and inquisitive 11-year-old, works as a potboy in his parents’ pub, The Trout at Godstow, and helps out the nuns living in the priory on the island across the way. He is an ordinary lad in some respects, but a golden boy over all – like Pip and Oliver in Dickens, with a dash of Kim, and of Emil from another classic Pullman admires, Erich Kästner’s Emil and the Detectives. As for Alice, she is seen, early on, working as a barmaid; when a customer pinches her bottom, she smashes a beer tankard and flings the handle at the offender.

One night, as Malcolm is watching great crested grebes nesting by the river, he accidentally observes a spy drop going wrong, and after that “everything just then seemed hung about with an unhappy air of suspicion and fear”. Pullman is a powerful voice for many endangered features of postwar society, which gave his (and my) generation so many chances. In Malcolm’s Oxford there are no free libraries any more; teachers are being bullied into dreary box-ticking; dissenting voices publicly humiliated and disappeared. The novel lets out an angry howl about climate change, inequality and criminal financial arrangements.On Pullman’s world map, however, the oppressors’ headquarters are in Geneva, the fountainhead of Calvinism, and of the doctrine of predestined damnation which Pullman has attacked so vehemently, while Uppsala in Sweden is the base of the organised resistance. The dreaded Consistorial Court of Discipline and its horrible offshoots are imposing full-scale surveillance and dreary intellectual compliance throughout schools, and urging children to denounce their parents for failing to conform. Worldwide, a craving for mysterious dust and its quantum possibilities drives the evil characters, and their machinations unfold in fractured glimpses as the mood grows ever more sombre.

Dakota Blue Richards as Lyra in The Golden Compass, the 2007 film adaptation of Northern Lights. Photograph: Allstar/New Line Cinema

Malcolm and Alice embark on a quest to save Lyra from Mrs Coulter, her enthralling, wicked mother, even more beautiful, cruel and terrible here, and deliver the baby to her father, the glamorous Lord Asriel, with his snow leopard daemon. The survival of the country is at stake, and the children’s ark gives the book its title. Six-month-old Lyra is a sweet baby, much less turbulent than the wonderful wild scruff of a girl who brought such dynamic excitement to the earlier books. She already has her daemon, Pantalaimon, a mischievous, furry shapeshifter, and Alice and Malcolm have theirs, too, also not yet “fixed” because they are young. These doppelgangers are Pullman’s greatest invention, and show his naturalist’s interest in animals, especially birds; Malcolm’s daemons are a twitcher’s dream – kingfisher, greenfinch and, for night vision, an owl. The chief villain, vampire-like in his lust for dust and other things, is a charmer when he wants to be, but a rapist and pederast with a monstrous hyena for a daemon, who is given to howling laughter and pissing in her victim’s path; she loses one leg in her first, frenzied fight with Malcolm and, later, another. This hellhound of twisted gothic fantasy is truly ghastly, and fulfils a point of honour for Pullman: no reader, child or other, need be spared. In imaginative fiction, sentiment, softness and sweetness are simply condescending.

Much mythological material is being brewed: a predestined wonderful foundling, a child snatcher, a few treacherously beguiling spectres and perilous fairylands. Pullman’s immense powers of kinaesthetic visualisation keep the story pulsing on an epic scale as enchanted allegory combines with a full-on retelling of the Biblical story of the flood: defences cave in and banks break under roiling storm clouds, and the familiar world of Oxford and its meadows is drowned.

But as the waters rise and the canoe is swept up on the torrent, the Victorian social realism of the book’s opening remains in force in Malcolm’s struggles to build fires to warm Lyra’s milk, and the surrounding scene spins into vague, turbulent dreams of English pastoral wrecked by malefactors and beset by raging monsters who must be overcome in ferocious combat. Again Pullman targets religious political authority and its hypocrisies: but this time he paints one convent in a kindly light compared to another, where the grim Sisters of Holy Obedience torment the orphans in their care. For more than half of the book, the deluge pours down so vividly I thought of putting on a mac and waders: “And the rain had set in with a fury. It fell not in drops but in sheets, and the ground was running with it, so that you couldn’t see anything solid: just flowing fields of bitter cold water ... ”

The Trout Inn at Wolvercote … the 11-year-old hero of La Belle Sauvage works in his parents’ pub. Photograph: Peter Brown/Alamy

When Pullman retold the Grimms’ Fairy Tales, he singled out for admiration their austere style, and quoted James Merrill’s yearning for “the kind of unseasoned telling found / In legends, fairy tales, a tone licked clean / Over the centuries by mild old tongues”. “Tradecraft” is a term that he uses admiringly here: the gyptians’ knowledge of the waterways isn’t eldritch, but expertise born of hands-on traditional work. The carefully wrought and mended canoe is itself a character, a daemonic ally more closely described in its physical materiality than any of the dramatis personae. Coram the gyptian explains: “Every inch of her has been looked at and strengthened … She’ll be the slippiest vessel on the Thames … She’ll go through the water like a hot knife through butter.”

Malcolm is handy, too: he helps the nuns fortify their convent against marauders, and there is even a chapter called “Glazing Sprigs” after the kind of nail needed to hold a pane of glass in place before pressing in the putty. He also works out the purpose of a carved acorn the spy network uses to pass messages: it does not unscrew in the usual way, but clockwise. Like the alethiometer, the truth-telling device that will become Lyra’s special clairvoyant tool, the subtle and contrary acorn captures the essence of Pullman’s methods. He likes to take received ideas – the sinfulness of the fall, legends of child-snatching Gypsies – and turn them round about and upside down until they ring false and hollow.

His declared aim is to re-enchant life for his readers, young and other, in order to withstand the pleasure-denying forces of political pieties and religious doctrine about sin and damnation. In a lecture called “The Republic of Heaven”, to be published next month in a collection called Dæmon Voices, Pullman speaks of his desire “to reclaim a vision of heaven from the wreck of religion; to realise that our human nature demands meaning and joy ... to accept that this meaning and joy will involve a passionate love of the physical world.” In La Belle Sauvage, the possibility of hope and love rises from the helpful knowhow of many admirable minor characters – carpenters and boatwrights, cooks and gardeners – as well as from the friendship of the two young protagonists and their courage. Alice’s character unfolds with touching surprisingness, and the passages about Malcolm’s confused feelings for her, as adolescence begins to change him, are among the most perceptive in the book.

Pullman himself is a woodworker, artist and calligrapher; his tradecraft aligns him with another important strand in the sensibility of Victorian Oxford and American transcendentalism: the independent-minded, visionary Henry David Thoreau building his cabin, William Morris with his ideals of beautiful handmade things, and John Ruskin, who shared those dreams. Pullman has come to resemble the Ancient Mariner, shaking hoary locks, demanding we pay attention to the calamities gathering on all sides. The radiant devices and other wishful dreams of alternative futures have rather faded from view in this new book, and the child heroes are beleaguered and alone in their valiant struggle against huge, massed forces of harm.

The tension in Pullman between deep attraction to magic and fierce atheistic pragmatism resolves itself into a commitment to art – especially shipshapeliness; this is a properly Romantic attitude. Just as his concept of daemons owes a lot to Coleridge’s ideas about inspiration, and his absolute trust in imagination rings with the hopes and beliefs of Keats and Shelley, so the commitment to the making of things as well as possible in the here and now expresses his faith that a well-made story, like the small, well-trimmed boat that carries the children on their long, dangerous journey, will offer shelter in any storm.

• Marina Warner’s Once Upon a Time: A Short History of Fairy Tale is published by Oxford. La Belle Sauvage is published by David Fickling. To order a copy for £14.60 (RRP £20) go to guardianbookshop.com or call 0330 333 6846. Free UK p&p over £10, online orders only.