An arcane but instructive way to evaluate corn ethanol, along with all biofuels, may not just be to audit their "net energy balance," but also their "net water balance." Evaluating whether or not a biofuel crop could be "water positive" is even more subjective to calculate than whether or not that crop is energy positive, but here goes:
Corn is one of the better temperate crops to use as a primary biofuel feedstock, since cellulosic extraction isn't here yet and sugar cane doesn't grow in Iowa. Using corn as an example, a good ethanol yield is about 480 gallons per acre per year, which is based on 160 bushels per acre, and 3.0 gallons of ethanol per bushel. How much water corn needs varies greatly, and the range we've arrived at for this analysis is between 300 and 900 cubic meters per ton. Our source for 900 m3/ton is from a reference to UNESCO's "The Water Footprint of Nations," and our source for 300 m3/ton is from Colorado State University.
Since a bushel of corn weighs about 70 pounds, based on a yield of 160 bushels per acre, expressed in tons the per acre yield of corn is about 5.6 tons. This means, at the lower figure of 300 cubic meters of water per ton of corn, the average acre of corn requires 1,680 tons of water per harvest cycle, which equates to 444,000 gallons of water for every 480 gallon yield of ethanol. Clearly, from this perspective, the 3-6 additional gallons of water required after harvest to refine each gallon of corn ethanol is not the critical factor - particularly when petroleum fuels also require water during their refining process.
If it takes 925 gallons of irrigation water to grow corn for every gallon of ethanol that can be distilled from corn, how much energy would it take to desalinate seawater to irrigate that corn? Would there be energy left over after the ethanol had been used to power the desalination plant that provided the fresh water for irrigating the corn? The answer is yes, but only when we use the lower figure - 300 cubic meters of water per ton of corn harvested.
Since 2.0 kilowatt-hours is necessary to desalinate a cubic meter of seawater, then at 300 cubic meters of water per ton, and 5.6 tons per acre, it takes 3,360 kilowatt-hours of electric power to desalinate enough water to irrigate an acre of corn for a year. Since ethanol has about 80,000 BTUs of energy per gallon, at a yield of 480 gallons per acre you will extract 38 million BTUs. Theoretically, 3,400 BTUs equals one kilowatt-hour, but even the best electric generating plants only succeed in capturing about 60% of those BTU's. This means that in terms of electric power, corn ethanol is good for about 23 million BTUs, equating to 6,776 kilowatt-hours.
So is corn ethanol water positive? At 300 cubic meters of water per acre, you would require 50% of your corn ethanol yield per acre to power the desalination plant to irrigate the corn. At 900 cubic meters of water per acre, your corn crop would not yield enough ethanol to desalinate the water required to irrigate the corn. Under these assumptions, growing and refining corn ethanol is certainly not a decisively water-positive enterprise.