The order the river suggests
Bagan, Luang Prabang, Ayutthaya, Siem Reap, Hue. It is not a single waterway you can travel end to end (Bagan sits on the Irrawaddy, not the Mekong, and Hue is on the Perfume River near the coast), but it is the order in which the region's history arranges itself, and it works as an itinerary.
Two weeks gives each city two nights and spends the rest moving. Three weeks is the version worth having: three nights in each, and time to take one leg slowly rather than flying it.
Seasons decide more than dates do
The cool dry months from November to February are the easy answer, and the busy one. March to May is hot enough to reorganise your day around the morning and the evening. The rains from June to October bring the landscape back and the river up, and the temples empty out.
Water level is the thing travellers underestimate. Low water exposes sandbars and makes some river crossings slower or impossible; high water is what the festivals at the end of the rains are celebrating.
What to book, and what not to
Book the long legs and the first night in each city. Leave the rest. The distances are short enough that a plan made on arrival is usually better than one made at home, and the good parts of this trip tend to be the ones you find out about the day before they happen.
If you want the slow boat between Huay Xai and Luang Prabang, that is the one fixture worth building the rest of the route around: two days on the water, one night at Pakbeng, and no way to hurry it.
