We have stopped at the Saitama Museum Of Rivers before, it is great and I highly recommend it. We didn't have that much time so we opted just to do the water play area, which you have to pay a bit extra for.
The main part of the museum is really good but I recommend that if you go, do that first and take a change of clothes because if you go in this section the kids will get wet. Lots of climbing, jumping, pulling, paddling and splashing....
