We did this last year (going upriver - Budapest to Prague) and enjoyed ourselves (hey - unlimited wine at dinner
Just note that if the river flow is either too much or too little, you may be put on a bus for part/all of your journey (beyond the bus from Prague to Nuremberg, which is overland, anyway). The week before we went, the river was running high due to a lot of rain and that group had to go partially by bus. On the upper reaches of the canal/river, you will not be able to go "topside" since they have to lower the railings and control house due to low passages under the bridges. Also, you will lose internet (if your boat has it available) during that time since the antenna masts must be also lowered.
Here's a picture going through one of the many locks you will see: