Two days traveling down the Rhine from cologne to mainz

Noel, Cologne to Mainz is UP the Rhine. It makes a difference because the boats travel faster downstream then upstream.

The timetable is here: http://www.kdrhine.com/rhineschedule.htm
Looking at the timetable, it is not possible to get all the way from Cologne to Mainz in one day. The timetable varies depending on time of year. The main section of the route is from Koblenz to Mainz (and vice-versa) not many trips go all the way to Cologne.

I think that you can book shorter cruises on some of the cruise boats. You do not have to go all the way.

I have done this in the opposite direction, down river. It was during the "prime" season, not shoulder season, and we did have to change boats along the way. The sights below Koblenz were nothing spectacular. The Remagen Bridge abuttments were of interest. Between Bonn and Cologne there is a magnificent petrochemical complex, if that is of interest. But the food and drink and company were good.

As Chris already says, Colgone to Mainz is up the Rhine and it's going to be painfully slow against the current. I haven't done a cruise, but I have done the trip from Mainz to Cologne on bicycle. The real interesting stuff is between Bingen and Koblenz, where the river goes trough the Rhine Gorge. The section between Mainz and Bingen is pleasant enough and the same goes for the stretch between Koblenz and Bonn. From Bonn to Cologne there is nothing special except the afromentioned petrochemical complex and also a nuclear powerplant if i remember correctly.
There are also trains running along both banks of the Rhine, so a combination of trains and boat could be an option. Fx take the train down to Bingen and boat it to Koblenz.
The best castles are Marksburg in Braubach, which is the only original medieval castle on the Rhine (the rest are reconstructions) and the Rheinfels ruins in St. Goar.

The nuclear power plant of Mülheim-Kärlich is near Koblenz. It is a sight! Why? Because it was built, and only used for 100 days. Because then a court declared the construction permit void because of not considering slight earthquakes prevalent at the place.

For a long long time that was the most expensive ruins ever built in Germany. We are now trying to top this with the new Berlin airport.

It would take an incredible amount of time to do Cologne-Mainz. And you'd be bored out of your skulls. Mainz-Koblenz (downstream) is faster but would not improve your psychological state.

"The real interesting stuff is between Bingen and Koblenz, where the river goes trough the Rhine Gorge. "

This statement is much closer to the truth. But I strongly suggest that you start in Bingen and end the cruise in St. Goar (downstream, 1.5 hours) or in Boppard (2.3 hours) as the scenery deteriorates as you approach Koblenz. If you look carefully at the KD schedule you'll see there are very few boats per day between many of the towns but 5 boats per day in each direction connecting Bingen-St. Goar-Boppard. That's because this segment has awesome scenery. Don't buy the KDRhine passes. Don't do a Viator tour. You can cover Bingen-St. Goar for about E20 or less - just buy your ticket at the dock. You can hop off and back on by getting your tickets authorized but IMO this doesn't work out so well as the schedule, even with 5 boats, is irregular. Just visit the towns by train before or after your cruise instead. Trains run hourly or better.

This is a fantastic area to spend 2 days. Just don't waste it all on the boats! Linz am Rhein and Remagen are north of Koblenz, great places to visit. But south of Koblenz is spectacular - Boppard, St. Goar (Rheinfels Castle), Oberwesel, and Bacharach on the west bank.... Braubach (Marksburg Castle) and Ruedsheim on the east bank... all these places are much more beautiful and interesting than you know at this point.

TRAINS: there are inexpensive day passes that cover every inch of train track between Koblenz and Mainz. Check out the column on the left here:
https://www.bahn.com/i/view/GBR/en/prices/germany/regional-offers-overview.shtml
(You're confused - don't worry - build a plan to visit the towns on specific dates and we'll assist you.)

Itinerary: I'd suggest 2 nights in St. Goar or Boppard - both are good base towns.
TRAIN ITINERARY:
Day 1: Cologne - (Remagen) - (Linz) - St. Goar / Boppard
Day 2: train to Bingen for morning cruise back to St. Goar / Boppard. Train to other towns, use St. Goar ferry or Boppard ferry as needed. These ferries run all day long between the river banks (no bridges.)

Mainz is a nice city if you have time for that too. Mainz-Frankfurt by train costs €8.25 each. Just buy a RMV ticket from a ticket machine in Mainz station.

We are now trying to top this with the new Berlin airport.

When the new Berlin airport opens, it will be old.

Why are you using information from Viator? This is a re-seller of tours run by other companies. They do not have their own tours. What ever info they have on their website is very limited and will only be about tours they are selling for some company. Don't use them.

Use the KD website for the ships, town websites for the castles and Deutsch Bahn for the trains.

Are you coming back to Cologne or going on from Mainz (presumably with luggage)?

If you are coming back to Cologne, where you leave your luggage, go up (southeast) the Rhein to Bingen Stadt Bhf, take the boat as far down the river as you want to, then take the train the rest of the way back to Cologne. But if you are continuing on, you probably want to store your luggage somewhere instead of going all the way back to Cologne to get it. There aren't very many Bahnhofs on the Rhein with lockers. Koblenz does have lockers; so does Mainz; neither Bahnhofs in Bingen have lockers.

If you stop in Koblenz, you'll probably have to wait an hour for the next train. There are hourly MRB trains from Cologne to Mainz. There are a few faster trains (REs and ICs) in between times, every two hours, I think, so you could take one or the faster trains to Koblenz, leave your luggage there, and take an MRB to Bingen (the faster trains don't stop at Bingen Stadt Bhf).

It would probably take you about an hour to go on from Stadt to Mainz, leave you luggage, and go back to Stadt, but you'll more than make up for that by taking the boat downstream.

Thank you everyone for the suggestions and for clarifying the flow of the Rhine. For some reason I thought it was running south and it is great to know we will be going the 'slow route'. We picked Koblenz to stay the night on this leg of our journey because it is in the middle (somewhat). So, it sounds like the most time effective way is to take the train from cologne to Koblenz then take the boats up and down river as we see fit over the two days. I went ahead and ordered the K-D passes and we will have train passes, so we have options depending on what we are feeling at that time of the trip. I have the feeling we will be doing a combination of train and boats. Also, thanks for the notes on lockers we are backpacking as we travel through Europe and will likely have our bags at least until we check into our place in Koblenz. So, I will definitely keep those as well as the castles/towns suggested in mind as we decide on where we want to stop off and check out along the Rhine.

"So, it sounds like the most time effective way is to take the train from cologne to Koblenz then take the boats up and down river as we see fit over the two days."

The advice you received doesn't sound like that to me. The suggestions above were to take the train to Bingen and cruise north from there for the most time-effective strategy and the best scenery. But if you've already ordered KD boat passes for two days at upwards of E120, it sounds to me like you prefer a whole lot of time on the boats.

"...it is great to know we will be going the 'slow route'."

If you are doing day trips by boat up and down the river from Koblenz, your southbound boat will travel the slow route and then the fast route on the way back; northbound, you'll first take the fast direction - then the slow one back to Koblenz. You'll be repeating the same scenery (which around Koblenz just isn't that great) on each outing. If time efficiency is a concern, then take the boat on the fast route and the train on the slow route.

If you make a stop at Koblenz and have tickets for K-D ships, consider going DOWN the Rhine from Bingen to Koblenz, then UP the Mosel from Koblenz to Cochem. K-D also runs ships there and they may refund your Rhine-upwards tickets for Mosel-upwards tickets. You would have additional sights.

it is great to know we will be going the 'slow route'

Arg! We'll see what you say after doing it. If all you want to do is ride a boat and the longer time, the better. But if you want to do some changing scenery, the boat with the current is fast enough (still slow). I knew which direction the Rhein flows when I went there, but I didn't fully understand the strength of the current, so I went upstream, from St. Goar to Bacharach. Never again.

it sounds like the most time effective way is to take the train from
cologne to Koblenz then take the boats up and down river

I seen heard people write that they like the town of Andernach itself, but I don't think the scenery down the river from Koblenz is that great.

I seen heard people write that they like the town of Andernach itself, but I don't think the scenery down the river from Koblenz is that great. Andernach certainly isn't the absolute highlight of the river, but it is a very pleasent town. I've never seen it's most famous attraction, though, the cold water geyser.

I agree that the scenery is best between Bingen and Koblenz, but once you get beyond some of the industrial areas north of Koblenz, the river is fairly scenic again until you reach Bonn. I also think the section from Rüdesheim to Wiesbaden is quite nice too, although quite different from the more famous strip just downstream.

Not much to see downstream of Bonn or upstream of Wiesbaden, however.