The Konigsee is a lake Southeast of Munich, crossed by an electric boat. I was there in early Autumn and it was one of my 'top 10' travel experiences. The lake was perfectly still, the trees were just beginning to change colors, the smell of wood smoke was in the air, and the tops of the mountains were barely dusted with snow. We stopped at a rustic church halfway up the lake, and had strudel and coffee outside under the trees. Doesn't get much better than that.
One hour south of Munich, near the Austrian border, is Königssee (King's Lake). Like a norwegian fjord the lake stretches over 8 km below the mighty Watzmann (2713 m). You can visit the chapel of St. Bartholomew on its eastbank by boat from Berchtesgaden. The chapel is an ideal starting point for hikes to the mountains.
The Königsee is one of the nicest lakes in the area, if the weather is nice take a boat to St. Bartholomä (it is not posible to walk there), a beautiful baroque chapel or to Salet (not in winter) from where you can walk to the Obersee. And take care the weather can change very fast, when i was there last the weather was great but i had to wait 30 minutes for the boat, by that time it was raining and one didn´t see much.
Get there from Munich by Bayern Ticket (€ 23 + € 5 for each, up to 4, additional persons, available at ticketmachines in trainstations) with frequent trains to Berchtesgaden where you change to bus 841.
Königsee at Berchtesgaden and the mountains around are splendid choices for experienced hikers. Don´t recommend day trips here, but longer routes.