A scorching morning in the San Fernando valley and I am driving up and down Balboa Boulevard, parks and fields either side of the motorway, lost. The talking GPS on my dashboard has lapsed into silence, defeated by an arcane destination with no zip code. I spy a park attendant emptying a bin and pull over to ask directions. He eyes me, baffled. I wonder if he is deaf and repeat the question. He still looks confused. "Did you say river?" Yes, I reply. Where is the river? He shakes his head. "What river?"

I find an elderly woman with a straw hat walking her terrier and ask the same question. She looks puzzled. "What river, honey?" The river I am supposed to kayak, I reply. She looks at me compassionately, as if I have sunstroke. "I don't think you're in the right place."

But I am. Swishing below, all but invisible from the park and motorway above, is the Los Angeles river. A river with water, fish, tadpoles, birds, reeds, banks, a river that flows for 52 miles skirting Burbank, north Hollywood, Silver Lake, downtown and Compton and empties into the Pacific Ocean at Long Beach. A regular river, except that to most Angelenos it's a secret. I ask three other people and receive the same blank looks until finally a park ranger confirms that, yes, there is a river at the bottom of a ravine all of 150ft away.

There, amid the reeds, bob a dozen little green and red kayaks, and people wearing helmets and lifejackets are clambering inside them. It is the inaugural season of LA River Expeditions, a pioneering effort to reclaim a waterway that vanished from the city's consciousness almost a century ago. "Welcome," says George Wolfe, the group's founder. "I hope you're ready for adventure." We push off into the current.

Until recently this excursion would have been considered not just mad but illegal. City authorities encased the river bed in concrete in the 1930s, turning it into a flood-control channel that was a byword for contamination and forbidden to boaters. For decades it languished all but forgotten, save for Hollywood using its storm drains in films such as Grease and Terminator 2. Now, however, it has formally opened to boating tours, specifically kayaks and canoes. Activists hope it is the first step towards transformation. "It's a milestone, and hopefully there are more to come," says Charles Eddy, a board member of Friends of the LA River, and part of this expedition, as he navigates his kayak through brambles. "If you think of the river as a blank palette, people will create all sorts of wonderful things."

Kayakers paddle under the Woodley Avenue bridge in Los Angeles. Photograph: ZUMA Wire Service / Alamy/Alamy

The kayak excursions are the latest twist in California's water wars, a saga immortalised in Roman Polanski's 1974 film Chinatown, a neo-noir exploration of intrigue and treachery with Jack Nicholson and Faye Dunaway set during the state's 1930s battles over land and water rights. The river, fed by streams from the Simi hills in Canoga park, originally provided food, water and transport for Gabrielino Indians and Spanish settlers. After the US seized control from Mexico the city's water needs outgrew the river. An aqueduct completed in 1913 directed water from the Owens river in the Sierra Nevada mountains to LA, ending dependence on the LA river. Disastrous flooding prompted its conversion – desecration, some critics would say – into a glorified drainage ditch. And so it remained for decades, a butt of jokes, a rubbish dump, out of sight and mind except when used as a backdrop for Hollywood car races and chases.

Its nascent revival this summer as a source of recreation and environmental awareness comes amid a renewed water battle. The diverted Owens river is no longer enough – LA county is home to about 10 million people, not to mention vast farms further south clamouring for irrigation. Governor Jerry Brown is championing a proposed $14bn (£9bn) tunnel system to divert water from northern California to southern California's parched cities and farms. Two tubes, each 33ft wide, would direct part of the Sacramento river – up to 9,000 cubic feet a second – to existing pumps and aqueducts, supposedly ending the water conflicts that Ronald Reagan, Arnold Schwarzenegger and a string of other governors failed to resolve.

"This thing is never going to be free of controversy and conflict," Brown told a press conference last month. "But we know a lot more today than we did then. Here we are, 30 years later, with a lot more knowledge and a lot more science." The US secretary of the interior, Ken Salazar, said the new tunnels would end "the epic water wars that have plagued this state for decades".

Maybe, but the plan will have to overcome resistance from environmentalists who say it will kill salmon and farmers who complain about costs. Some analysts think the water wars will drag on, with southern California seeking ever more desperate remedies for its water shortages.

LA as a "soulless, dystopian metropolis": Terminator 2: Judgment Day. Photograph: Tristar/Sportsphoto Ltd/Allstar

The Los Angeles river, once the city's lifeblood, is a sideshow to the latest high-powered struggles for water. But to a coalition of artists, historians, environmentalists and outdoors enthusiasts its fate symbolises an attempt to make LA, branded by critics a soulless, dystopian metropolis, a kinder, gentler, more integrated city.

"We have to start thinking in new ways, and using words differently. If you call it a sewer ditch you treat it like a sewer ditch. Call it a river and you treat it like a river," says Wolfe, the expedition leader, as our group paddles upstream through a gorge. An advertising copywriter with a passion for canoeing, Wolfe and some companions made the first journey down the entire river over three days in 2008. It was technically illegal – the city did not want anyone in its drainage ditch – but they rebuffed police challenges with a (legitimate) filming permit, a magical pass when dealing with the LAPD, and made it to Long Beach.

The voyage obliged authorities to admit that the waterway was navigable, something previously denied, and created a legal wedge to demand public access under public trust doctrine, a concept dating from Roman law. Eddy says 80% of the water was treated sewage, most of the rest groundwater with modest contamination. "My dog has been drinking it for seven years and he hasn't got three tails."

Inch by inch, authorities yielded, allowing Wolfe and his friends to take 300 people down the river in a pilot project last year. After nobody drowned or contracted a hideous disease, LA River Expeditions was allowed to start running regular, scheduled trips this summer for around 2,000 people. Tickets – $55 (£35) each – were snapped up within minutes of going on sale. "So here we are," says Wolfe, as the group of mostly novice kayakers bump and splash in his wake along a narrow stretch of surging water. The mood is giddy. Like the park attendant and dog-walker, until recently some of us did not even know there was a river, or where it was, or that it was usable. "I've lived near this river almost all my life and I've never been on it. I jumped at this chance," says Gloria Barke, 77, a retired events organiser, as her partner Robert Finkle, 81, a copyright lawyer, paddles from the back.

The LA river will never compete with the Danube or Seine or Thames as an attraction for stressed city-dwellers. Nor will it inspire many poems or novels. It is too meagre, too hidden, to ever be fully part of the city. But advocates are on to something when they say it can transform perceptions of LA.

After passing a concrete bridge with graffiti-daubed arches and a shopping trolley half-buried in mud, we enter a wilderness that seems a world removed from the freeways and urban sprawl above. "We call this the Grand Canyon," says Wolfe, showing his flair for advertising, as we paddle through a mini-gorge 15ft tall. Nature slowly asserts itself. To our left are wild fig trees, descendants of those planted by the Indians, to our right potentially deadly ricin-producing plants. Further on, hallucinogenic jimson weed. "Around the next bend is the Apocalypse Now bit," says Wolfe. We encounter "fish sticks": improvised traps made by unknown hands to trap carp, tilapia and other species. A discourse on how to make the traps is drowned out by a passenger jet roaring low overhead, briefly breaking the spell.

The sense that this is something special returns as we moor our boats and slosh ashore, inspecting plants, a turtle shell, a cascade, before resuming the journey. It is difficult to believe that the 405 freeway, the gridlocked bane of LA motorists, is just a mile away. Three hours later we return to where we started, a swampy bank, and moor the kayaks amid some ducks. The tour is over. We saw nothing that would excite David Attenborough. But we glimpsed another LA, one not consumed by automobiles, or turned into a strip mall, where nature and human optimism thrive in a watery realm, an ever so slightly mystic river.

• This article was amended on 3 September 2012. The original referred to hallucinogenic gypsum weed. That should have been jimson weed, or Datura, and has been corrected.