I'm just guessing here, because I don't know how much of the cost fuel is, but the river cruises are one-way, and much shorter (for instance, Budapest to Vilshofen is around 550km) where as the Adriatic Expedition Cruise is round-trip to Venice, and the one-way from Venice to Kodor is (very) approximately 900km, for a round trip of 1800km. So well more than 3 times the distance. So that would cost way more for fuel. And maybe Ponant just charges more than AmaWaterways does to use their ships & crews? Again, just guessing here.
ETA:
It's not really almost twice as much. The 2 lowest categories of cabins on the Adriatic cruises are sold out, so you can't really compare the "starting at" prices to the lowest category on the river cruises. A lot of the river cruises are at like $5400 for the lowest price, which, while much less than $8800, is not half. But yes, it's pretty pricey.
Sayhello