Trying to see specific places on the Middle-Rhine can be frustrating, since crossing points are limited. With so many things to see on both sides of the River, use this guide to get the most out of your day. This is targeted mostly for people interested in taking public transport, an option I recommend in this region. Driving makes some destinations more accessible. However it may only make things more complicated given the limited options for parking and the high volume of traffic.
Modes of Transportation
There are four main modes of public transportation on the Middle-Rhine: the railroad connections on the left bank, those on the right bank, ferries and the cruise ships.
1. Rail connections on the left bank
The only high-speed rail services in this region travel on the Mainz-Koblenz-Bonn stretch on the left bank. This is the optimal way to travel to Koblenz from Mainz, as it reduces travel time by over an hour. Travelling from Bonn, the difference is less noticeable given alternative regional-express options. Travelling in the upper (southern) left bank of the river by regional train is difficult. The schedule can be infrequent and some stations are serviced only a few times a day. The main tourist destinations of Bacharach, Oberwesel and Boppard (Not St. Goar!) are easily reached with an hourly service. In the lower (northern) bank, the trains run every half-hour or every hour.
2. Rail Connections on the right bank
All of the towns on the right bank up to Neuwied are serviced by a single rail line which travels on an hourly basis: Frankfurt-Wiesbaden-Koblenz-Neuwied. To travel from Frankfurt to Neuwied takes about 3 hours, so this is not the recommended way to reach Koblenz. However, it hits every stop every hour and is thus fairly reliable. Past Neuwied the train frequency drops depending on the day of the week. Both Remagen and St. Goar can be reached by ferry via Erpel and St. Goarshausen respectively.
There are a lot of ferries on the Rhine, notably in Rüdesheim (to Bingen), Kaub (to Pfalzgrafenstein), St. Goarshausen (to St. Goar) and Erpel (to Remagen) and others. These can be used to see specific things on the other side of the river. They can also form complete circuits with the train home on the other side. Some things like Pfalzgrafenstein can only be visited via Ferry.
4. Cruise Ships
Despite being cruise ships, due to the regularity of their operations you can use them in lieu of other forms of transportation. They will stop at most of the interesting destinations anyway. In fact, your local train-timetables-app will probably list available cruises if they offer the shortest way to reach a destination. In addition to their tourist function, another important service is getting you home when the train gets cancelled. You can check the schedules easily online.
Planning your Trip
Seeing all of the best locations will probably require multiple days. For limited schedules though, there are a number of plausible ways to travel easily between some locations. Depending on your preferences, one strategy could be to start on the right bank coming from Rüdesheim (or Frankfurt) and stop initially in Kaub. While there, see the Pfalzgrafenstein, then take the train to St. Goarshausen. From there cross the river by Ferry to St. Goar, see the fortress ruins and the town, then take a cruise. On the boat you can travel back to Oberwesel and/or Bacharach to enjoy an evening glass or Riesling. From there you can take the train home.
Indeed for a more intense travelling day it is possible to start in Mainz and work your way up from Oberwesel to Boppard then to Koblenz and back down the right bank. Or instead, continue north and return to Koblenz for a high speed return trip to Mainz.
Trying to visit any number of specific castles is made more complicated by the time it takes to reach them. The famous two, the Marksburg and Pfalzgrafenstein are right next to the train station. In comparison, some like Rheinfels and Stolzenfels will require more planning. This is the case where using a car might offer some advantages. Though during tourist season, the road infrastructure and the number of parking spaces is severely limited, and the region is a very popular destination. Be sure to do some homework on what do with the car when not driving it. St. Goar for example has a huge parking lot both above and below the town. Trying to park in Kaub will probably end up being a nightmare, perhaps it will be better to park elsewhere and take a train.