If you're coming from Germany, probably the best way to get to Stein am Rhein is by bus. DB Bus 7349 departs roughly hourly from Singen, making multiple stops on its route to the Stein am Rhein train station. In our case, the bus stopped at Stein am Rhein - Strandbad, which was only a few steps away from the youth hostel, where we were staying. When we departed, we took the bus from Strandbad to the train station. You pay your fare to the driver on the bus, payable in Euros or Swiss Francs. Even on our short trip to the train station, we were able to pay in Euros, which allowed us to get rid of a few more Euro coins. On the bus route, there is a 50% discount to the fare with a valid Swiss Pass.
One important note: The bus stop in Singen is rather hard to find if you're in a hurry. The buses to Stein am Rhein depart from Bus Stop F, which is located across the street and about 100 meters to the left from the Singen train station. Unfortunately, we were unable to locate the stop in time, so we missed the bus, and had to wait an hour for the next one.
Stein am Rhein has a small train station on the south side of town. Local ("S-Bahn") trains depart for various destinations regularly, including Schaffhausen, Winterthur, Rorschach, and St. Gallen. In addition, Deutsche Bahn operates buses which run between Stein am Rhein and Singen in Germany (though some early/late buses only go as far as Ramsen).
Services are modest at the station, but include a shop and an SBB travel center (where you can, among other things, validate your railpass).
I can only speak about Stuttgart > Stein am Rhein here, but if you're in Baden Wuerttemburg, you could take a day down to this beautiful part of Switzerland.
If you want to take the train from Stuttgart, the fastest way is to change at Winterthur or at Singen. This will take about 3.5 hours in all. The scenery will be fabuluous! :)
There's three main ways to go to Stein am Rhein :
By the road :
By car the trip from Zurich takes less than an hour. Head north on N1 until a point near Winterthur, where you connect with E41 going north to Schaffhausen. This route becomes N4, connecting with Route 13, heading east toward Stein-am-Rhein.
By train :
Stein-am-Rhein lies midway along the railway link connecting Schaffhausen with Kreuzlingen, on the edge of Lake Constance. From Zurich, passengers take an express train to Winterthur, then change for a less frequent local train to Stein-am-Rhein; trip time from Zurich is just 1:20 minutes.
The Cost is 19.80 chf one-way
More info : Swiss Federal Railways
By Boat :
The best line is from Schaffhausen - Konstanz / Kreuzlingen. There is 4 starts from Schaffhausen (9:10, 11:10, 13:10 and 15:10) The journey is 2:05.
The Cost is 19.60 chf one-way and 29 chf return.
More info : Untersee und Rhein
The full price return ticket between Stein am Rhein and Zürich costs 44 CHF. Where as the full price one way ticket is 22 CHF. The journey takes about 1 hour.
A few full price return journey train fares from Stein am Rhein are following:
1. To Geneva: (4h 23min) 167/- CHF
2. To Bern: (2h 36min) 108/- CHF
3. To Lugano: (4h 15min) 132/- CHF
4. To Basel: (2h 2min) 91/- CHF
We drove straight down from Stuttgart to Ramsen (CH) first then Stein am Rhein was only a short drive away.
It is about 2-2.5 hours from Stuttgart.
There are many possibilities to make different cruises along the Rhine river, and they are all beautiful.