(Compare with the shortage of cows and chickens. What shortage, you say? Exactly. It is managed by the owners of the cows and chickens so there's a ready supply.)
Government regulation is a lousy solution, as it will allocate the resource based on politics, not practicality, efficiency, or common sense. You see this as well in California - regulating showers with ineffectual results.
One way would be to allocate X gallons per year total can be pumped, and then auction off those gallon rights.