Bruges, Belgium to Burgundy and Alps!

It's going to be challenging to connect all these dots in 9 days and have any time left over to sightsee. But if you take the train to Colmar (6-7 hours) you can go Colmar > Beaune > Chamonix > Annecy and fly home from Lyon.

You could drive or take the train from Colmar to Beaune. You'd definitely want to drive from Burgundy to Chamonix if you go that route, but you might reasonably decide to return the car in Chamonix since it will only be a hindrance there.

I think you should at least consider what a trip with fewer destinations might be like. Slow down and see more. Perhaps 1 wine region or 1 alpine destination. Your conspicuous omission any mention of Paris suggest you are not interested in spending any time there, but Paris + Burgundy + Chamonix (not necessarily in that order) would be spectacular.

Note that both Alsace and Burgundy offer superb cycling and there is no better way to get a feel for the land.

It's true that France borders Belgium, but it's eight hours by car and 1000km to Chamonix from Bruges. Would it make more sense to select an area closer to Belgium? I shouldn't make any assumptions, but since you're coming off a packaged tour, will you be willing to put in the intense planning needed for the complex itinerary you're proposing?

Certainly the wines are different from Beaune, but we spent six days driving from Strasbourg to Besancon, with some wine-tasting (but no hiking) along the way. You might consider that many better wineries require reservations for tastings. I assume you're less interested in bicycling for the last 9 days. But all European countries have lovely national parks and plenty of hiking. We prefer long walks in historic cities, but I'm not proposing that you do that instead.

There are lots of gorges and river valleys in France that might serve your needs without going so far. For example, we saw some beautiful landscapes in the Jura. And we saw hikers from the hilltop citadel in Besancon. Since I recently became winded during some simple hiking in the Park City, UT area, you might want to consider the elevation in Chamonix, and then after taking a cable car.

To save time maybe take a train from Bruges to Colmar then rent a car from there? We drove Lille to Gray back in Sept. It was around 5 hours driving time with 2 short breaks. Once in Colmar you are looking at shorter car trips from there to Beaune, then over to Annecy.
Beaune, Annecy and Chamonix are worth seeing. I've never been to Colmar but it is on our list.
Geneva is a nice airport to go in and out of. We used it when visiting our daughter in Grenoble.

Diane -
My wife and I just did the Chamonix-Annecy-Beaune-Lyon part in September. We took a shuttle from Geneva airport to Chamonix (about 45 minutes) and spent 4 days hiking the Alps. If you are into hiking, do not skip this. Unbelievable views of Mont Blanc and the Alps. Annecy rightfully is called the Venice of France, and also has remarkable scenery. We rented a car in Chamonix and after Annecy, drove to Dijon where we left the car. It's about a four hour drive. We then self-guided bike from Dijion to Beaune over a six day period. The biking through the vineyards, especially on the VelloRoute through Nuits St. George, Vosne Romanee, Morey St. Denis, and Gevrey Chambertain, was wonderful. There are plenty of places to rent bikes in the small towns.
Lodging highlights included The Hermitage in Chamonix, Hotel Cloches in Dijon, and Le Cep in Beaune. Do not miss the light shows in Beaune.
Larry

If traveling from Bruges to Colmar by train, I'd avoid changing trains in Paris, because you have to cross town to a different station, as well. There is currently a departure from Bruges about noon that requires just one train connection in Brussels. (You can leave Bruges earlier, but plan to catch the direct InterCity from Brussels to Colmar about 13:00). How to Look Up Train Schedules Online gives you the DB train schedule link and tips for using it.

Picking up and dropping a car within France, even at different cities, is cheaper than an international rental. If dropping the car at Geneva airport, be sure to specify the French side of the airport. You might not be able to do this online (e.g., with Auto Europe) but can do it with their phone agents.

Pick up the car somewhere in France. . . you may have more options in Strasbourg than Colmar. You could return the car in Chamonix after touring through Switzerland, then take the shuttle to the Geneva airport.

I'm currently looking at a 5-day stay in Alsace and everything points to having a car.

Thank you all for your help! We are now thinking of flying from Brussels to Geneva after our biking/barge trip, as cost is reasonable, under 80 euros. Then picking up a car in Charmonix, after doing the hiking in the Alps we so desire for 3 days. ( Thank you Larry for the advice about that! ) Then driving on to Annecy 1 night, Beaune 3 nights and Colmar 2/3 nights. Possibly leaving car in Strasbourg and taking train to Paris to fly home. Plane flights seem to be more of an issue than ever! We have traveled through France in Sept. 2013, and rented a car for 17 days, Paris/Normandy/Provence/Nice. So feel we are up for this trip! The Barge/Bike tour is actually our first packaged tour we've done, after going to Europe now our 7th time! Always with Rick, in our back pocket! When in these wine regions, do you just tour on your own? Are reservations needed? Are there tours you could suggest? When we were in Provence and the Dordogne we just drove up to the vineyards and sampled, purchasing a bottle was usually around 10-15 Euros. Love help on the trip! Thanks.

Re reservations: You are traveling in high season, so the answer really depends on you. Calling morning of to reserve can work if you are flexible about where you sleep, but I do mean flexible.

Tours are available (at least in Burgundy) but not required. A car or bicycle will get you out to the vineyards.

There is a tasting lunch in Aloxe Cortone (near Beaune) that I recommend, and reservations would be a good idea in June.

Note there is an early direct TGV from Dijon (or Beaune with a connection) that will deliver you to Charles deGaulle by 9 AM, plenty of time to make a flight home. So you might consider planning your trip to end there; there's nothing similar from Alsace.

Adam
Thanks for the TGV info! That is what we were looking for. Should work out if we stick to this itinerary. We usually travel in the shoulder season, so do want to get going on reservations for this June trip! Imagine the TGV we would have to reserve? The lunch/tasting looks very inviting too, will keep that in mind. Biking to the vineyards, would interest us. Although after the biking/barge trip and alpine hiking the beginning of the 3 weeks…we will play it by ear there I think!! Thanks.