Not on the Altmühl, but near where the rivers join, one of my favorites is a walk along the Danube from Kelheim past the Befeiungshalle on the hill, and then up the hill through what was a Keltisches Oppidum (Roman history here too), back down the hill to get to the small boats that ferry you across the Danube to the Weltenburg Kloister for beer and lunch (the Kloister brews it's own famous beers). Then take the cruse boat through the gorge on the Danube back to Kelheim. It can be done in a half day. I think the small boats will still be ferrying in September. You can always just take the Danube boat to and from Kelheim to the Kloister. http://www.weltenburger.de/en/
http://www.schiffahrt-kelheim.de/
http://www.naturfreunde-kelheim.de/Aktivitaeten/Wandertipp/Wandertipp%20Kelheim-Weltenburg-Kelheim/Rundwanderung%20Kelheim-Weltenburg-Kelheim.html You only have to walk halfway there, so 4-5km.
Berching and Beilngries are nice cities too worth a visit. I like walking along the Main-Donau-Kanal in Berching. You can get a beer here: http://www.brauereigasthof-winkler.de/
I would recommend Gausthof Sitrzer in Dietfurt for a really nice dinner. Lamb is famous in this region. http://www.stirzer.de/ Make reservations!
For the kids there is a Sommerrodelbahn near Riedenburg www.altmuehlbob.com/ There is a rope bridge near Riedenburg that could be fun for the kids too.
Kipfenberg has a Roman and Keltin museum and the Roman wall Limes went through the town. http://www.bajuwaren-kipfenberg.de/ The castle is private but looks great from below.
A little out of the way but Regensburg is worth the visit http://www.regensburg.com/ The old town is a UNESCO World Heritage Site. Check out the 500 year-old historical "Wurstkuchl" for a bratwurst semmel (sandwich) with sweet Händlmaier mustard by the old bridge. http://www.wurstkuchl.de/tavern.html Look for the high water marks on the "Wurstkuchl." Get a beer at one of the Kneitinger Gasthaus (local Regensberg Brauerei). I like the one on Arnulfsplatz 3 http://www.knei.de/ This is really local...
I can recommend Eichstätt too. Its famous for the churches and their varying architecture. http://www.eichstaett.de/
Neumarkt is farther to the north and not all that much to see, but the church there has the best bells I have heard in Germany. Be there at noon. Wolfstein castle there is kind of neat too. If you have gone this far north you might as well think about visiting Nürnberg another of my favorite Bavarian cities. My favorite beer garden in Nürnberg is at the Krakauer Turm http://www.restauration-kopernikus.de/ Make reservations on the weekends. Another favorite place is Beim Tiergärtnertor near the giant bronze rabbit sculpture from the Albrecht Dürer painting. The Albrecht Dürer house is nearby. Take the tor gate out of the old town, then walk north around the moat and then back into the Nürnberg castle. Nice views of the castle wall and the walk is not as steep as directly up from the market place.
Anyway, nice relatively easy places for walks and bike rides through the Altmühltal. Altmühltal would be a nice relaxing week away from many non-German tourists. Consider a Ferienwohnung (FeWo rental apartment) to base out of with the kids.
