The Urdaibai Bird Center has been cutely styled like an international airport terminal, with multilingual boards marked Arrivals and Departures, and a raised observation platform resembling an air traffic control tower. Through a roof-mounted telescope I watch various avian species landing or taking off from little floating archipelagos on the adjoining lagoon.

I am not a birder so I don’t know what they’re called, though I do recognise the (grey) heron by its pterodactyl flight profile.

Rowan Hardman, the centre’s environmental educator, points out lapwings, greenshanks, bank swallows. Her favourites are the spoonbills: “They’re big, white and dramatic, but also calm and static, always sleeping or preening. They reflect how this marsh has become a peaceful haven for them.”

This quiet corner of northern Spain, at the coastal edge of the Basque Country, is now a regular stopover on southward migration routes from the UK and Scandinavia to sub-Saharan Africa (then back again come spring).

“We’ve got the Bay of Biscay to one side, the Pyrenees to the other,” says Hardman, a Briton from Portsmouth who relocated here 30 years ago. “So the birds are funnelled into this flight corridor between them, and we’re part of a chain of habitats along the way, like service stations.”

Since opening at a former cannery in 2012, this facility has been a success story in reclaiming and rewilding a previously dried-out, chewed-up agricultural tract. A different order of development is now planned just across the wetland, so close you can see it through the telescope, where a shuttered shipyard will soon be repurposed as one of two new rural annexes of the Guggenheim museum – that gleaming showcase for modern art in nearby Bilbao. On the train from Bilbao, I passed through towns and villages strung with banners opposing the project, though Hardman can’t comment beyond the bird centre’s official line: “We are not anti-Guggenheim, we are pro-preservation of the marsh.”

The primary remits are research and outreach. A nifty, kid-friendly interactive museum on the ground floor maps migration patterns and relays seasonal birdsongs through a geodesic echo chamber. There’s a small hotel on the upper level, too, with six simple double rooms, a breakfast buffet area and a private birdwatching lounge. Its appeal to “twitchers” is obvious.

One entry in the guestbook reads: “I’ve never spotted so many species without taking my slippers off.” However, Hardman says the serious hobbyists tend to go their own way, with their own gear, seeking out the rarest sightings. A majority who come to sleep on this site are less specialised, more all embracing, “basically, nature lovers”.

Long intervals during my own visit are spent thoroughly distracted on a low sofa at the back window, which is roughly the size and aspect ratio of a cinema screen. The birds seem almost incidental to the picture, as the light and weather make their slow transitions. Waves of mist roll down the deep green mountains soon after dawn; gold sunbeams flare off white wingtips at roosting time; an autumn moon shines over the flat black pools near midnight.

All seems eternal out there, though I’m also told of old Franco-era plans to remake the surrounding Urdaibai estuary as a northern Costa del Sol, with leisure marinas and high-rise hotels along the banks and beaches. Residents petitioned the Basque government, and eventually secured Unesco protection as a biosphere reserve in 1984.

In the 40 years since, that status has drawn a less invasive sort of tourism: hikers, cyclists and kayakers exploring a tideland of cliffs, capes, holm oak forests and fertile floodplains. When the Cantabrian Sea swells in autumn, surfers come to ride one especially long wave that breaks over the river-mouth sand bar outside Mundaka harbour.

The food alone is reason to visit, and the neighbouring port of Bermeo has been declared “Tuna World Capital” by a local business alliance dedicated to sustainable fishing. I feel obliged to try some at Rola, house restaurant of the Hotel Nafarrola, recently opened by two Bermeo-born siblings at a former dairy farm on the mountain above town.

“‘Sustainability’ can mean many things these days,” says Josu Goikoetxea Larrauri, while I eat an immaculate tuna tartare prepared by his brother Gaizka, a chef who trained at San Sebastián’s fine dining institution Zuberoa. “To us it means fish from this harbour, meat from this valley, txakoli from small bodegas close to us.” That signature Basque white wine fills much of the cellar they built outside, and the field out front will soon be a small vineyard. In the garden, we catch uninvited goats stealing precious Hondarrabi Zuri grapes already planted. They will not leave quietly, and Josu calls the farmer to come and drag them home.

The bells round their necks sound loud and clear across these slopes, as indeed do occasional peals from medieval chapel bells on surrounding peaks and promontories. Next morning, I climb the 241 stone steps to the ninth-century hermitage at San Juan de Gaztelugatxe, overtaking a few exhausted nuns on the steep, narrow coastal causeway.

In midsummer, pilgrims ascend to ring the bell three times, conferring blessings on the brave souls who work these waters. Cristina Krug is one of those, a local anthropologist turned river guide who drives me back up the estuary on her motor launch, a decommissioned naval patrol boat she bought online and had painted in friendlier colours.

Born and educated in Bilbao, Krug moved here to marry a cargo ship crewman – and has since heard all the abiding myths of ancient mariners. The clanging bells of early Christians are said to have scared off the lamiak, an indigenous subspecies of mermaid from native folklore, who drowned or saved sailors according to their whims.

“Basque language and culture are so much older than in other parts of Spain, and even Europe,” says Krug, navigating us around sandbanks and salt meadows. “I don’t think Catholicism ever fully took hold here.”

She tells me about bone picks and shells excavated from the nearby Santimamiñe caves, just north of Guernica, where early mollusc farmers moved into the former home of Palaeolithic ancestors who painted aurochs on the walls. To Krug, it seems that a somewhat pagan spirit prevails in this watery place and its people.

Fishing is in deep decline now, she says. More jobs and revenues are needed, and are promised by the new Guggenheim outpost, along with assurances of minimal environmental impact. Anecdotally speaking, Krug says residents are dubious: “We know better how delicate this ecosystem is. But nobody asked us.”

For now, peace prevails at the bird centre. On the path across the marsh I sit down inside a wooden hide and lose the twilight hours checking birds I see against their pictures on the wall. It bothers me, as I get older, that I don’t know the names for all the beautiful things of this world. But here they are in Latin, English, Spanish and ancient Basque. The coot is kopetazuria in that language. The teal is zertzeta arrunta. The mighty osprey is arrano arrantzalea, though one solitary male is known to the team as Muxar.

He’s never been banded or tracked, but Muxar has returned for the last seven autumns, and become so comfortable that he spends the winter here, never flying any farther south. The distances are so vast, the hazards so great – who would not stay right here if they could?

Local rail network Euskotren operates trains from Bilbao to Forua, the closest stop to Urdaibai Bird Center. Doubles at the onsite hotel from £80pp (two-night minimum stay) via booking.com. Dinner at Rola is reserved for guests of the Hotel Nafarrola but open to the public for lunch by reservation. Cristina Krug operates estuary tours from £16pp an hour