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Is Lake Wolfgangsee or Lake Mondsee a better place to spend a couple of nights, and what is the reason that one is better than the other.

Wolfgangsee !
More scenic, better villages, larger.

I thought Wolfgangsee and Mundsee were right next to each other, guess I'm wrong. Which lake is the prettiest, Mundsee or Wolfgang Lake?

I would also recommend Wolfgangsee, for the reasons stated by Bob the Navigator, and also because it has the better boat service. Furthermore, Mondsee has roads close to almost every part of the shore whereas Wolfgangsee has car-free trails in some parts - much nicer for walking. Wolfgangsee is completely surrounded by mountains, Mondsee is not. They are indeed very close to each other, however. Thus, if you have a car it probably makes not much of a difference. If you travel by public transport, Wolfgangsee is more convenient.

Also Wolfgangsee is the prettier overall, although Mondsee has a beautiful church.

Girlfriend and I stayed in Mondsee for a week on a choral singing course, culminating in a concert in the very beautiful church in the centre. [setting for the wedding in the Sound of Music]As well as the singing rehearsals, we had some day trips, one of which was to Wolfgangsee. It was much prettier than Mondsee and more interesting. So, unless you have a buring desire to stay where the sound of music was filmed, I wouldn't bother!

Suze1:

You are correct . . . it's only a few KM between Mondsee and Wolfgangsee, but the Wolfgangsee is far prettier, has good ferry service between St. Gilgen and St. Wolfgang, two of the best towns to visit on all the lakes in the Salzkamergut. The surrounding mountains are awesome . . . not so at Mondsee, and from St. Gilgen you can take the cable car to the top of the Zwölferhorn Mountain http://www.12erhorn.at/ for a spectacular view over the lakes and perhaps have lunch while watching the para-sailors. Mondsee is nice but much more vanilla. The very busy Autobahn A1 passes within a stones throw of Mondsee somewhat dampening its charm. Unless you're smitten by the fact that the wedding scene in the Sound of Music was filmed in the beautiful church at Mondsee, you'll be far better satisfied staying at St. Gilgen or St. Wolfgang. You can always visit Mondsee for a couple of hours by local transportation and stay based on Wolfgangsee.