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As the water taxi budged its way through the labyrinth of canals one grey Wednesday recently, I knew what was coming. Up ahead, at my hotel, was a porter, on the dock, holding out a pair of knee-high black rubber boots.

I slipped them on, squeaked my way clear of the boat's mahogany frame, and sloshed my way through the lobby's ankle-high inundation until I washed ashore at the reception desk. Someone handed me a glass of prosecco, as if to congratulate me for my nautical accomplishment.

For people who actually live in Venice, a dozen centimetres of water on the floor offers no such sense of adventure. The romance of living in a 1,300-year-old city built on wooden stakes driven into the mud floor of a lagoon is dimmed by the floods, which take place at least 100 days of the year, usually starting in November. Battered by tidal surges from the east and river influxes from the West, Venice is the world's first city – but certainly not the last – to know what it's like when the sea is reaching your knees.

Here is a city whose private life takes place upstairs, its ground floors largely abandoned to the waves – especially after the terrible flood of November, 1966, when 194 centimetres of water destroyed much of Venice's ground-level grandeur and launched a project that, today, every maritime city in the world is watching. Venice's flood season, after all, could soon be Mumbai's, Miami's, Halifax's flood season. Many scientists believe global warming and melting ice caps will cause ocean levels to rise 10 to 30 cm. So when we visit Venice today, we are visiting our homes tomorrow.

I had come here to watch this city save itself, once again, in the most stupendous nature-challenging effort that has taken place here since the Italians first fled the Barbarian-colonized dry land to raise palaces here in the 700s.

But I'd also argue that the rain-and-flood season, when Venice is most empty and most itself, is the best time to visit this city, to discover that beneath its centuries of tourist clichés is a living, real city with good food and real neighbourhoods. And that by poking around carefully, in the backstreets and abandoned ramparts that are hidden from gondola-riding canoodlers, you will find much to learn about life in a world of rising waters – and you'll have a chance to see a stunning salvation in the works.

The elegant woman at the desk of the hotel, built recently in a glass-merchant's 15th-century palace that had lain empty for decades (in other words, a typical hotel here), sighs and tells me she's counting the days. “This is unbearable – you can't live, you can't welcome guests when there's water everywhere,” she says. “They just have to hurry up and finish the Mose.”

She's referring to the portentously named MOdulo Sperimentale Elettromeccanico, a project whose acronym – Moses, in Italian – is as overcooked as its budget of $7-billion, its timeline of 30 years or its ambition of defying nature and stopping the tides. For most Venetians, who have long since accepted their city's becoming a theme park-cum-museum as its only path to salvation, its 2011 completion date cannot come soon enough.

For other Venetians, deeply wary of anything that touches their ancient ways and equally distrustful of anything coming from the government of Italy (which many here still see as a foreign country), nothing good can come of it. Strolling the back pathways and bridges of Venice, you'll see the graffito “No MOSE” painted on walls. In the view of Mayor Massimo Cacciari, a rumpled philosopher given to fistfights with his less co-operative constituents, the whole thing is a conspiracy to destroy the purity of his city and turn the lagoon into a stinking toilet. Or, rather, into more of a toilet.

For visitors, this is your chance to witness an experiment that may define the next century. Moses is a grand effort to regulate the tides entering the lagoon, by building enormous air-driven floating valves that can stop the water while allowing the largest container ships, up to 70 metres wide, to pass through a huge system of locks.

“This is your only chance to see the beauty of this construction,” chief engineer Alberto Scotti says. “After it is finished, it will be completely invisible, except the few times of year when it is operating, when all you will see is the mysterious sight of the water being higher on one side and lower on the other.” All the works will be buried beneath the waves. Mr. Scotti notes that there is a deep dilemma behind his project: It must not interfere with the natural environment, in a place whose entire “nature,” from the shape of the lagoon to the flow of the rivers, was created by humans. It is a triumph of humanity over the cruelty of nature – that is the greatness of Venice, and if it works, it'll be the charm of Moses.

I took a boat out to one of the lagoon's three entrances to see it at work. I chose the northern entrance of Lido, whose tide barriers must be built to handle most of the Mediterranean's cruise ships passing in and out. Each has its own challenge: The central entrance of Malamocco must handle endless cargo-container ships through vast locks. And the southern entrance of Chioggia has to endure an entire Adriatic fishing fleet. At Lido, through the drizzle, a dozen huge cranes loomed over the water, countless tugboats and industrial craft toiled away, and a huge pile-driver barge pounded away.

The world is suddenly very interested in this project. The government of New Orleans has paid it a visit. And over the summer, the government of Singapore announced that it would start working on an even larger project, designed to protect the city state from any foreseeable rise in water – and Moses is their model. (Moses is meant to protect Venice from a permanent 60 cm sea-level rise as well as a three-metre flood, while still allowing shipping.)

Moses is being built exactly as Venice was. For centuries, Venetians drove thousands of logs into the mud to create city-wide platforms that substituted for land; the grandest palaces and largest houses of Venice simply sit on top of these logs, with no other means of support (which is why the climax of Casino Royale, with a Venetian palace sinking into the lagoon, is probably impossible). This new marvel is being built with steel-and-concrete piles, and without interfering with nature in any way – all the construction takes place on artificial islands that will house the controls – but it is familiar to most Venetians.

If you want to see this project at work, you could take a boat out to one of the three lagoon inlets to see the heavy lifting going on – there'd be a lot of explosive action, since millions of tonnes of huge boulders and odd-shaped concrete blocks are being dumped into the sea to form breakwaters. Or you could head out to the Adriatic side of the Lido, where the beach, eroded to nothing by rising tides, has been impressively reconstructed using millions of tonnes of sand as part of the Moses project. It's a splendidly empty stretch in the off season, with the lonely ambience of empty beach resorts.

But if you really want to feel Venice change beneath your feet, and see its impossible structure and its explosive history in one stunning tableau, I would instead spend a day that is part of every visit to Venice for me.

Take the vaporetto – the crowded water-ferry bus that is the city's only form of public transit (until a proposed subway beneath the lagoon is built) – past St. Mark's Square and the overcrowded drama of Venice's golden-age splendour and get off at the little-visited stop of Arsenale.

Step inside the Arsenale district, which until not long ago was a military stronghold forbidden to visitors, and enter a very different Venice. This military shipyard, which essentially froze in time when Napoleon invaded at the beginning of the 19th century, houses a huge-scale Venice: great dry docks from the 1600s, encrusted in lions; hulking, half-kilometre rope factories from even earlier times, seemingly abandoned last week; towering, rusted steam cranes shipped in from Manchester in the 1870s, resembling ghostly Dr. Seuss animals.

Some of these buildings are used to host the city's vast art and architecture exhibitions (the Biennale is taking place until mid-December), allowing you access to some of the most secret and secluded corners of Arsenale, with the added benefit of great art.

But when it's lonely, this is the best place to see Venice at work. At the north end of the Arsenale are the workshops for the Moses project. Here, crews are assembling the huge air-buoyed tide stoppers, metal hulks the size of office towers that will be shipped out by barge and dropped into the ocean, never to be seen again. And here, soon, will open an interpretive centre devoted to this engineering monstrosity.

When you return from Arsenale to your hotel, skip the vaporetto. Walk instead through the far backstreets of Castello, the central island of Venice, and then into the even more murky, more surprise-filled alleys of Cannaregio, allowing yourself to get lost for a few hours, or a couple days, in these residential quarters.

At 4:30 in the afternoon, wherever you are, join thousands of other Venetians and stop at a side-street bar for a bitter aperitivo and a tiny prosciutto sandwich. Allow the locals to distract you: On a visit last year, an off-duty water-taxi driver led me on an extraordinary stroll through half-metre-wide backstreets and water-hopping passages of Castello, finally entering a bar and having a fistfight with an unruly regular to defend my honour. Then, after I thanked him with a brandy, he showed me his favourite secret restaurant, an invisible, dimly lit place that made impeccable grilled dorade, the king of Adriatic fish. On the way back, I was yanked into foreign-colour detail by a group of Venetian teenagers who partied in flagrant abandon on the back deck of a back-island vaporetto, giving me a very different tour of their city. Such experiences actually do happen in Venice – if you keep yourself far away from the pigeon-feeding masses, in the far more interesting residential quarters.

And while you're back there, you have your chance to see how Venice really works, in sun and in flood. Look at the way the ground floors are built and supported – the ancient, impeccable supports are fully visible here. Look at the rot setting in, the completely abandoned lower and top floors of many buildings (Venice is being depopulated), the jury-rigged bids to keep the water out, the stonework that seems to be holding forever, the shocking ornamental details in places where nobody could possibly want to look. Watch what the less wealthy residents of these back quarters are doing, and think what would happen to your neighbourhood if its streets became canals.

Venice becomes a far more beautiful, more haunting place if you give yourself over to its underside. I'd strongly suggest you spend your nights in the back quarters of Cannaregio, whose laundry-strewn lanes offer the best views of the city's heroic construction, the most genuine neighbourhood moments, the most unprepossessing hotels, and the best local food at canal-side eateries – only a 10-minute walk from the noisier sights of the Grand Canal. On the way out to the airport, having seen what is perpetually disappearing beneath the waves, you can get a glimpse of the cranes on the skyline, saving it all from the inevitable.