travel from Munich to Lindau can't book online

Forget RailEurope. It's an unnecessary middle-man that doesn't even show you all the train options available. Always use the websites of the national rail operators, which in this case for Germany, is Deutsche Bahn.

Use the German rail booking site http://www.bahn.de/p_en/view/index.shtml and type in Munich, you'll see flughafen as an option, and Lindau. You should see lots of times and 1 change routes in the 23-29€ range. If your date to travel is further away than 90 days, that may be why you don't see fares yet. Use the bahn.de website not the rail Europe site for best prices and more routes.

Not sure why you are having trouble finding connections at RailEurope, but don't use them anyway. Use the Bahn website. The Schedule and Fare webpage is at http://reiseauskunft.bahn.de/bin/query2.exe/en. Other links will get you here eventually; start here.

Any connection from the Munich airport will have to have a connection in Munich, from the local S-Bahn to the direct train to Lindau. There is a connection that leaves the airport at 9:24, changing in Pasing (12 min), getting to Lindau at 13:16.

It's generally unwise to book cheap saver fares for use right after a flight - you forfeit the ticket if your flight is late and you miss the train.

But you don't need a full priced ticket either. You don't even need to book. After exiting security just walk to the airport train terminal and buy a Bayern Ticket from a ticket machine for the trip to Lindau. This day pass is valid anytime on Sat or Sun, after 9 am weekdays, on local and regional trains.

If you end up missing your anticipated train, you can catch a later one that day with a new set of connections.

Thank you everyone for your responses! I should have included that I have a three country eurail flexi pass (Germany France and Switzerland) and was trying to reserve my journeys that require them. I will need to get online and reserve without the middle man! Any further advice is most welcome and thank you again.

The route through Kißlegg is "permissable" but not any faster and has many changes of trains. I would just take the direct train from the airport to Muenchen Hbf to Lindau via Immenstadt.

Don't bother with the flexipass from Munich to Lindau. Use the Bayern-Ticket. It's 23 euro for one, 28 euro for two people. Save the rail pass.

Most connections to Lindau are by regional trains and you can't reserve them. There's a reservable EC connection at 11:33, but unless you are ready to leave MUC between 10:33 and 11:33, it wouldn't be worth taking it.

Yes, the Bayern Ticket allows you to save a day here - a good choice. You should be careful to avoid the connections that get to Lindau with ULM as a stop, however, as they drag you out of Bavaria and your ticket won't be valid.

The direct train RE 57408 train at 10:20 from Munich's main station would be very convenient. But it doesn't actually stop in Immenstadt, or in Kempten, as far as I can tell, Lee. Are you sure that it takes the 975 route and not the 971 (Kißlegg route??) It's the same with the direct 14:20 ALX from Munich to Lindau. I am unable to find any direct trains to Lindau with Immenstadt as a stop.

I'm thinking that the Kißlegg route (in Baden-Württemberg) is designated a Bayern Ticket route because this route is an important one for certain trains (probably the direct trains above) heading to Lindau from Bavaria.

Geltungsbereich: https://www.bahn.de/p/view/mdb/pv/deutschland_erleben/allgemein/tickets/2015/mdb_177012_141214_bayern-ticket_geltungsbereich.pdf (see 2., Hergatz-Wangen-Tannheim-Memmingen)

I've been on that route from Lindau to Immenstadt and from Immenstadt to Munich many times in the past 16 years. This is a new twist for me. Apparently this summer, from today until October 20, they are working on the tracks between Immenstadt and Oberstaufen. Some trains are being rerouted from Memmingen through Kißlegg to Hergatz. Others are being rerouted from Immenstadt by bus (SEV) to Oberstaufen. After Oct 20, the train from Munich to Lindau will go through Immenstadt. The Kißlegg route is not usual.

Several times, I have gone from Aulendorf to Kißlegg to Hergatz to Immenstadt. Hergatz is a very small station on the route from Immenstadt to Lindau. In 2002, when I first stopped there, there was no underpass from track 1 to track 2/3. We came from Kißlegg into Hergatz on track 3, a stub track. The train from Lindau to Immenstadt came into Hergatz on track 1.

While we were changing to the Immenstadt train, a train from Munich to Lindau came in on track 2. To get to the train to Immenstadt, we had to go through the train from Munich. Really!

German trains don't require a seat reservation with your rail pass. The afore-mentioned DB web site is the best source to see when a train is Subject to Compulsory Reservation. Among your three countries, those are only likely to be trains to, from, or within France and those are best booked ahead through Rail Europe to ensure that you get the departures you want. If your trip has connections, only reserve the portion that requires it. (You may need to break the route into its pieces for reservations, anyway, since Rail Europe's search engine usually can't handle more than one connection on a request.)