A: Enviromental concerns could be a problem.B: The costs could be more, or at least equal that of terrestrial space, plus have a longer time to develop and consruct.

So how are you going to keep this giant air bubble under the water? And if its very large in a small lake, won't it disperse the water in the lake?

Using water for warehousing could be augmented by a different design. Instead of enclosing the warehouse, enclose individual objects or shipments. If you water-proof a shipping container, for example, you can weight it to neutral bouancy. Then you can move it around with very light machinery.

I tend to think, however, that the whole issue may be made obsolete by just-in-time inventory management.

I've had a similar idea for some time. But I think a better use than warehousing would be an undersea research and industrial facility. Once a Kevlar-reinforced, transparent synthetic "bubble" membrane is anchored to the sea floor and filled with breathable air, permanent structures could be erected inside to provide a "shirt sleeve" work environment. Regular visits by submarine cargo vessels could stock the facility with fuel, food, breathing gases, and other supplies for the workforce. Commercial submarine vessels could use the facility as an undersea port to restock, rotate personnel, even have light maintenence and repair work done.

If your plan was in a marine environment, what about earthquakes? Seems to me that anything anchored to the sea floor would be hard to protect.

Regardless of whether it was marine or fresh water wouldn't it take a lot of energy to pressurize breathable gasses?

If the structure is at a fairly deep depth, it will be necessary for visitors to undergo lengthy decompression procedures to avoid the bends. What's the advantage of using inflatable structures instead of rigid ones? If you use concrete, the structure will be stronger, heavier(which will reduce the tendancy to float), and will not need to be pressurized, elliminating the need for airlocks or decompression.