I have always been under the impression that going downstream is better - you know, "going with the flow". In the grand scheme of things, though, I think either direction is fine. Cruise lines have designed the itineraries with the direction in mind. You generally have same port stops and of course the same scenery. So the decision is really personal preference.
However, there are a few small and a few major
differences regarding the direction which may be important to you.
A ship must naturally work harder when sailing against the current. The stronger the current, the harder the engines work, which may translate into added vibrations from the engines. During the day or evening dinner this isn't really noticeable, but it can/will be while sleeping. Likewise, the closer your cabin location to the engines the more likely you are to feel the vibration. On my Danube trip I was on a lower deck towards the middle of the ship. We didn't have a strong current, so the vibrations were subtle and actually lulled me to sleep. Friends on higher decks didn't feel anything. They felt the bump in the lock, but not the engines.
Sailing with or against the current impacts schedules - meaning the time the ship arrives and departs a particular port. When sailing against a current it will take longer to get to the next port. Sailing with the current gets you there faster, especially if the current is strong. Although much of the sailing is done at night, if the itinerary has daytime sailing (for example, sailing through the Rhine Valley Gorge or Wachau Valley on the Danube), one may spend more or less time in a particular port. Another consideration is that most of the rivers have locks, and ships have to "get in line" to go through. On the Danube cruise our captain told us that ships sometimes have specific times they must go through, and if they miss that time slot they must wait for an opening. So if the ship is going against a particularly strong current, one may not have as much time in a particular port in order to make the time slot.
To expand a bit further on the above, timing has an impact on time spent in port versus sailing. Going upstream lends itself to more sailing time while downstream lends itself to more port time. Some people would rather spend more time exploring a town. Others would love to spend more time sitting back and relaxing, watching the scenery go by. The time differences aren't huge but may be noticeable. What do you prefer?
In my opinion, river currents make a small difference in the "direction to take" decision. The following, I believe, have a bigger role:
Preference in starting and ending points
I have clients who, at the end of a cruise can keep on exploring, while others are somewhat weary or time constrained and need to get home. If you are in the latter group, embark in the city that is of most interest to you. Take advantage of pre-cruise time and the general excitement of the trip. On the other hand, if your preference is "leaving the best to last", end the trip with what you consider to be the best sites and cities.
Sometimes one city is better than another from an arrival or departure perspective. This is normally not an issue when spending a few extra days pre and post cruise, but transportation schedules may dictate which direction is best for you. One destination may have a more circuitous route than another. You may not mind having more transportation segments at the beginning of the trip but would prefer the shortest way home at the end of the trip.
This is sort of a given, but sometimes you are limited by the dates available - either the itinerary itself or your own schedule.
In summary, when it comes right down to it, which direction to take on a river cruise has a little to do with the river currents and a lot more to do with personal preferences.
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