Travelling by boat along the rhine

K-D has several scheduled runs a day between Cologne and Mainz. You can just buy a ticket for the leg you want every day. You might even inquire if they allow a multiday hop-on-hop-off. Travel south to north as it is quicker running down stream. The section between Rudesheim and St Goar is always crowded with sightseers from the world over taking in the Rhine gorge. Koblenz is worth a stop to ride the cable car over the Rhine to the old fort on the bluff above Koblenz. You can also take side boat trip up the Mosel a ways. Also the train to Moselkern and hike up to Burg Elz castle (an RS favorite, and for good reasons). Lots of people like Bachrach, St Goar.

"We'd rather be more flexible and stay in each city for a few days."
A good idea. With 2 weeks, it would make sense to spend 4-5 days in maybe 3 different towns - and take outings from those towns to other places - by boat, if feasible, or by train. You should have a look at the K-D boat schedule - it will give you some clues about which parts of the river are worth seeing by boat. http://www.k-d.de/english/kd-scheduled-cruises/kd-rhine-timetable/ If you do, you'll find that in high season, in the 44-km section between Rüdesheim and Boppard (the most scenic section) there are 5 boats per day in each direction. North (from Koblenz to Linz) and south (from Rüdesheim to Mainz) of this section, service drops off quite a bit because the scenery is much less interesting. Notice that service between Linz and Bonn picks up quite a bit. Linz is a fabulous town, and this part of the river, though less dramatic, has some very pleasant scenery. The "best places to visit" will depend on your interests. On the Rhine, I would probably pick Linz as one base town, and Bacharach as a second. From Linz, outings to Bonn, Cologne, and Remagen are very doable (but a look at the schedules will tell you that Cologne is best visited by train.) From Bacharach, you can do outings to St. Goar (Rheinfels Castle), Braubach (Marksburg Castle), Boppard, Oberwesel, and Rüdesheim. Then I would spend 4-5 days on the Mosel River - probably in Cochem, where numerous outings by cruise boat and train are possible. http://www.kolb-mosel.com/en/tours.php

Thank you. I'll check into the K-D boat schedules. We're definitely planning on visiting Koblenz -we were in Cochem in 2011 but the locks were being repaired so we weren't able to travel far by boat. We travelled by train through Koblenz but are planning to visit there for at least a couple of days. Thanks again for your help.

I have great memories in the gardens at the Konisbacher brewery in Koblenz watching the tour boats go by. If you happen to need accommodations, Bavaria Ben has good writeups in this website: http://www.bensbauernhof.com
Bacharach is a great little town to stay in.