read the ones that do this with tanks that are right next to eachother that have a 'water bridge'. From what I remember, they are a PITA to get the water in the tube. I cant image how they'd do it in this one.
You could put some sort of blockage on the entrace/exists with some sort of 'door/block'. Then at the top, fill it with full with water. Then let go of those doors/blocks to let fish enter/exit. But you'd have to make sure that at all times that those tubes stayed under the water.. if not.. bye bye water into one tank.