Suzy, that's a hard question to answer. I can only give you a hint about our experience. We took the Great Rivers cruise in July 2006. Everything was fine except for the record heat wave we had while there. It was not bad on the ship, but during our extension in Vienna we suffered a bit with the heat. The crowds were not at all objectionable. Well, Rothenberg and Heidleberg were a bit crowded but the rest of the tours were great.
In May 2010 we took the Romance of the Rhine and Mosel cruise. It was cool to cold and rained nearly every day. It was still a great cruise. We were closer to being dressed for the cool weather than we had been for the hot weather on the GRE cruise. The rain and the cool did not interfere with any touring, although it made some of them a little less enjoyable than they might have been. But, to show how fickle the weather might be, that same year April had been warm and dry, so we were told.
In August 2011 we encountered the fact that all of Europe was on vacation. It was not a GCT cruise, but we were on a cruise of the Baltic Sea. The crowds were horrendous in every port and nearly half of the passengers on the ship were families with young children. It will take some extraordinary circumstances to get me to Europe in August again. It would have no impact on the shipboard conditions, but might impact some of the ports and the included shore tours.
As to water levels, we had no problems in either July or May, but that is not say the same would be true in 2014.
This is not very helpful but it's the best I can do. Go and have fun, when ever you decide to go.