When the deck hand waved at me, I gave a shy little wave back. The crew on board the Premicon Queen had been nothing if not friendly, so I was left reflecting to myself on the intimate bonhomie of river cruises. Then he gave me a really big, rather more urgent, wave: he was doing a sweep of the top deck to warn us of fast-approaching low bridges, for which Germany's Main river is renowned.

These, and the number of locks that mark the progress of the Main, mean it is one of Europe's lesser-known waterways for pleasure boats, yet it is now becoming more popular. This is in part because it joins the two classic European cruises: one the "romantic route" that links the castles of the Rhine; the other down the Danube, via capitals such as Vienna, Bratislava and Budapest (the river's Hungarian section is currently under threat from the toxic industrial spill earlier this week). And that is thanks to the Rhine-Main-Danube Canal, connecting the two great river systems of Europe: the Rhine in the west, the Danube in the east. The notion of such a link dates back to Charlemagne, but this feat of engineering was completed only in 1992.

On a six-night cruise from Frankfurt to Regensburg, I found that, far from just being a transfer between the two better-known rivers, the filling in the sandwich proved to be its most pleasant surprise. As soon as the skyscrapers of Europe's Manhattan (as some call Frankfurt) disappeared behind us, we were bound for some of central Europe's finest gems: the medieval cities of Franconia. The attractions of the Main are one reason why tour operators are starting to offer two- or three-week cruises from Holland to Romania, which take in all three rivers.

A few years ago, you would either have been brave or foolhardy to attempt such a voyage. The shake, rattle and roll of quaint-looking, old-fashioned boats (and their tiny cabins) meant that wise travel agents would recommend that you spend as many nights on dry land as onboard, if only to get away from the noisy generators. But with river cruises becoming increasingly comfortable, there is now no reason why you shouldn't go all the way. And no ship is more comfortable – or silent – than the Premicon Queen, launched two years ago.

Elegant in its own swan-like way from the outside, it is positively luxurious from the inside. Not only is it impressively spacious and – with its lift – accessible to wheelchair users, but the cabins have sliding French windows opening on to the river. And, unlike on many such craft, I struggled even to notice when the boat was underway, as just the slightest slap of water on the hull indicated we had reached our first stop, Miltenberg.

A pretty town dating from the Middle Ages, Miltenberg is reckoned to boast one of the oldest hostelries in Germany, with the emperor Barbarossa its first guest. And Franconia, or Franken to the Germans, is known for its wines, so wine-tasting is included in this excursion. The ship's sommelier and butler also came ashore to buy local wine – sold in its traditional, flask-shaped bottles – for dinner that evening. From the restaurant, I watched as the steep, mountainside vineyards with their strict geometric patterns cascaded down to the beaches of the Main, where swimmers were ending their day splashing in the water. Well into my fifth course, I felt rather envious of their sporting prowess and so, after dinner, joined them in spirit in the spa's water-level whirlpool, where I felt almost as if I was in the river.

The next morning, I woke to find that we had already berthed in Würzburg – a place ringed by castles, churches and more vineyards. A medieval university town with no industry to speak of, it survived the Second World War virtually unscathed until 16 March 1945 – just 21 days before the city surrendered – when it fell foul of the Allies' "Casablanca Directive" to flatten every German industrial city of more than 100,000 inhabitants in order to weaken enemy morale.

There was no note of recrimination in the commentary that accompanied our tour – just a tremendous pride in the rebuilding that took place in the 1950s. And indeed, when you look at the rococo façades, it's amazing to learn that the town was almost recreated from scratch. The one part that did escape virtually intact is the baroque palace, which locals rushed to protect. It's easy to see why: an indulgence built to rival Versailles, or Schönbrunn in Vienna, it is full of trompes d'oeils so intricate that even after studying the ceiling for several minutes I could not tell what was a statue and what was a fresco.

A dearth of English-speakers on this trip meant the shore-based tours were only available in German – in fact, most passengers opted anyway to wander ashore under their own steam. However, the Premicon Queen's onboard commentary is always relayed in English, too, and the staff are bilingual. In between the pomp and ceremony of a gala dinner (the culinary artworks so impressive I felt my spoon hovering before it swept in to destroy them), the cruise director explained that the ship is one of a few to cater for non-German speakers.

The history of the mountainside castles is intriguing: sometimes their owners would string ropes or chains across the river to raid boats or demand tolls. But the most absorbing thing about this journey is the ever-changing backdrop. We would race water-skiers, cyclists and canoeists heading for the rapids, while, on the stiller reaches of the river, boys would wave to us before showing off their somersaults and dives into the water.

Nevertheless, the Main is a working waterway, as our mooring in Bamberg, in the city's industrial zone, reminded us. The centre of Bamberg is a 10-minute taxi ride away, and reveals itself to be, like Würzburg, another buzzing university town. It's also – again like Würzburg – a World Heritage site. It survived the war relatively unscathed, and there are many more higgledy-piggledy half-timbered houses here inbetween the Baroque gems.

At Bamberg, we were breaking new ground as we joined the Main-Danube Canal. Even though it is nearly 20 years old, only a few of the larger river cruisers are designed to be able to navigate it, so we felt like pioneers as we cut through the landscape, on a seemingly endless series of locks which carried us to Nuremberg the next morning.

The city was almost entirely destroyed in the war and – aside from the thick city walls – had to be completely rebuilt. Below the surface, though, stretching downwards as far as 100 feet, are cellars cut into the rock more than 1,000 years ago to cool beer. These were used to protect the art treasures of the city.

Regensburg was our third World Heritage site in about as many days. By now, we were on the Danube itself, passing under the arches of the 12th-century bridge that hops over the fast-flowing river and then berthing near the maze of the town centre. The town also marked our last stop: it was time for me to leave my waterside room for good and rejoin real life on the river bank.

Travel essentials: Main cruise

Getting there

* The writer flew as a guest of Lufthansa (0871 945 9747; lufthansa.com), which flies from Heathrow, Birmingham, Manchester and Edinburgh to Frankfurt, with one-way fares starting at £49. The same fare applies between Munich and Heathrow, Birmingham and Manchester. British Airways (0844 493 0787; ba.com) also flies to Frankfurt, and BA and easyJet (0905 821 0905; easyjet.com) fly to Munich.

* Munich airport can be reached from Regensburg by train (08718 80 80 66; bahn.com/uk) with the Bayern Länder-Ticket. This offers unlimited travel for a day within Bavaria for up to five people (after 9am weekdays) for €28.

Cruising there

* The Premicon Queen (0049 421 3336 182; premiconqueen.de) is sailing on the five-night cruise between Regensburg and Vienna, with the price per person starting at €1,295. The next cruise between Regensburg and Frankfurt is from 19 to 25 October; prices start at €1,575 for six nights.

More information

* German National Tourist Board: germany.travel