when you say bavarian lakes, where do you mean? cheimsee, the biggest lake in bavaria sitting just before the alps? worthsee, big lake nestled in the hills? starnberg/ammersee, big lakes south of munich, about half-way between munich and the alps? or bodensee (lake constance), the biggest lake in western europe?
there is really good biking around tegernsee/schliersee/bayrischzell. it is where bionicon test their bikes. the train network is fairly extensive meaning you can do point to point rides as opposed to loops.
mtb-news.de sign up and ask on there. just write in english as most can read it. think there may be some routes already on the site.
i'll have a trawl later but i've got to go out and look for work right now....
bis nachher.