There are two ways the bladder could expand and contract. One way is by stretching the material (like blowing up a toy balloon). The other way is by the material "folding up" (like a half-inflated airbed).
I was thinking of a fairly substantial "membrane" (e.g. like an inflatable boat) so the stretching would be small. There doesn't seem any advantage in making the pontoon out of a stretchy material, just for the sake of it.
Either way, I would be worried by significant changes of volume because of possible stability problems. If the pontoon sinks lower in the water, the water pressure increases and its volume reduces, therefore the buoyancy reduces and it sinks further.
Another design issue is that the only way a membrane (with no bending stiffness) can support a load is by having a curved shape. Presumably you want your pontoon to have a flat top, and flat bottom - otherwise it would be deeper to displace the same volume of water and give the same buoyancy. So you probably need to make it from a raft of cylinders not one big bladder. That would also be good for safety, since a local puncture would be less likely to sink it.
Personally I would design it to be pressurized so it was effectively rigid. The water pressure at the bottom of the structure is about 0.1 atm per meter depth. Assuming your pontoon has a depth of the order of 1m, an internal pressure of say 0.5 or 1.0 atm should be enough to do the job. You would still have the advantages of easy transportation etc.