High winds, horizontal, driving rain and cold, choppy seas have turned Sydney Harbour into a riot of grey.

"It's what you might call a typical 'wet arse, no fish' sort of day," says skipper and historian Gregory Blaxell, peering philosophically through the gloom at a passing RiverCat as the water at the deep end of the tinnie begins to lap over his boot-tops.

Indeed it is. The first of the "one or two showers" forecast is reducing my notebook to papier-mache, waterlogging photographer Mike Bowers's camera gear and threatening to turn we three would-be river rats into drowned rats.

In literary terms, a relatively light-hearted "three men in a boat" excursion to explore Sydney's lesser-known bays and backwaters suddenly seems like a daunting expedition into the heart of darkness.

An excursion that was supposed to resemble a chapter from The Wind In The Willows - Toad, Ratty and Mole messing about on the Parramatta River - looks more likely to end in a scene from The African Queen , with us being ignominiously towed home. Anything but that.

After less than two hours on the water, the great adventure is abandoned. Or, rather, merely postponed. Wimps maybe but we were still men on a mission to boldly go.

To sail in the wake, to walk in the footsteps of Arthur Phillip, Australia's first governor, who followed the Parramatta River and its feeder creeks in search of farmland.

To make our own Nile-style expedition to find the river's source, somewhere hidden, reportedly high above Baulkham Hills.

To rediscover a waterway with a fascinating past and fraught present that remains unknown to many Sydneysiders. For to travel up the river today is to tumble back and forth through the pages of Australian history, to visit places whose very names provide clues to their part in that history.

Some are Aboriginal, such as Wallumatta, Cabarita, Yurulbin and Parramatta. Some, such as Hen and Chickens Bay and Snails Bay, have their origin in geological features, natural biology or, in the case of Kissing Point, a naval term indicating the diminishing depth of the estuary. Many more hint at the waterway's history since European settlement.

Using charts prepared by Captain John Hunter and Lieutenant William Bradley, who had earlier reached the navigable "head of the harbour", The Flats at Homebush Bay, Phillip made his way upriver.

After camping overnight at The Flats, they proceeded to a branch in the river. They rowed up the Duck River, which they thought was the main channel. Realising their mistake as the tide dropped, they retreated and returned to Sydney Cove.

Phillip returned in mid-April, one of a team of 11, each carrying a knapsack of provisions, that "put you in mind of a gang of travelling gypsies". No Gore-Tex macs. No big Tohatsu outboard motors. But unlike us, the governor did not allow a small spot of bad weather to delay him.

Undeterred by north-westerly winds, thundery squalls, temperatures wallowing in their mid-teens and bad health, "brought on by cold and fatigue", Phillip explored the upper reaches and headwaters of the river.

For several days, he travelled north and west up the river, through what he named the Crescent, and along the freshwater section of the Parramatta River until they reached Toongabbie Creek that, with the Darling Mills Creek, becomes the river.

He followed the creek until it turned north, whereupon he struck out west, leaving the waterway. He eventually reached Bellevue (present-day Prospect Hill), from which he could see clear across the Cumberland Plain.

He soon concluded that Parramatta - or Rose Hill as he named it in honour of a civil servant, George Rose - should be the fledgling colony's principal city, because it was surrounded by good farmland and was impregnable to "enemy naval bombardment".

Within a year, the first locally built boat - officially named the Rose Hill Packet but known as The Lump - was running from Sydney Cove to the new settlement.

The trip, on a boat crafted by convicts and powered by sail and oar or pole, involved negotiating hazards such as The Flats, a stretch of shallow water near Homebush. It could take days. Today's RiverCats take 55 minutes from Circular Quay.

The river was probably more relaxing, possibly far quicker, cheaper and less dangerous than taking the Parramatta Road, infested with escaped convicts. Indeed, the road has been a nightmare, on and off, since it was opened as early as 1793.

We laid fanciful plans to emulate Phillip. As he did in 1788, with three small boats borrowed from the Sirius, we would travel upriver in rowboats or even kayaks, camping, or staying (for the purposes of research, of course) in old waterside hotels, or even brothels.

Perhaps we could even catch and cook our own food. After all, hadn't the intrepid Phillip dined, typically, on bread, a kettle of soup cooked from white cockatoo and a couple of crows, kangaroo pie, teal duck stuffed with salted beef and plum duff, washed down with wine and rum?

Such pipe-dreams are quickly extinguished. A kayak would be sheer madness, a rowboat totally impracticable for a river trip that measures, by the main channel, about 19.5 kilometres.

And that did not take into account the many planned diversions. Or the possibility of being hit by a big north-westerly that could blow small, unpowered craft backwards. Or, despite the estimable Blaxell's seamanship, our lack of 18th century ferry-fitness.

Other snags emerge, like floating logs in the river of our dreams. There never were riverside brothels. There were two pubs: Montgomery's Palace on the waterfront at Mortlake and The Malting Shovel, site of James Squire's and Australia's first brewery, upstream at Putney. The first moved, the second is long gone.

The river is closed to unauthorised craft upstream of Silverwater Bridge, where it narrows to run through the mangroves. However, Sydney Ferries says it is possible to negotiate a time-slot that allows you to avoid its services.

More seriously, as anyone who has used the RiverCat would know, a weir and other man-made barriers, including an impossibly low bridge, would prevent us from making our way upstream from Parramatta. Again, the local council offers help if, say, we want to launch a kayak in the CBD.

And, then there's the freshwater section of the river and beyond that Toongabbie Creek. It may sound bucolic and, remarkably, parts will prove to be still so. But as Google Maps, street directories and local expert John Carse, suggest, though it runs through several reserves, it is not always easy going along its 13.8 kilometres.

Navigable, though in many places only on foot, here and there it disappears down concrete pipes and culverts, reappearing from beneath roads, housing developments and industrial estates, before eventually running off the map altogether.

And its source? "Probably, no more than an indentation in the ground somewhere," says Carse, the Parramatta-based acting general manager of the Sydney Metropolitan Catchment Management Authority, as he points north towards Castle Hill.

So it was that, just two days after a miserable false start, Blaxell, Bowers and Huxley set sail in a 14-foot tinnie, this time trying to beat strong north-westerly winds and temperatures in the mid-30s in an expedition up the river.

In the spirit of Ludwig Leichhardt, or Burke and Wills, we were determined to complete the journey from our official starting point - a line drawn across the harbour from Longnose Point to Mann Point - to its source.

Even if it meant doing it in sections, getting rid of the tinnie, switching to something smaller or simply walking.