It very well may be that Nestle (and many other companies) are under-paying for their water rights, but I don't think you're comparing apples to apples.
Disclaimer: Nestle are utterly evil
Well, when you phrase it that way it sounds terrible, but it's a completely bogus comparison. A retail water user is paying not just for the water but more importantly for it's storage and delivery to their doorstep. That increasers the price. You also are not buying in bulk. If you were, you would only be paying $50-200 an acre foot as most California farmers do to have water stored and delivered to their farms. Nestle is only paying for access to a water source. Is $524 too low a fee for a permit? Yeah, probably, but the company isn't "stealing" water, and compared to what farmers pay for similar amounts of water isn't not that that different.
The federal government is charging Nestlé $524 for 36,000,000 gal of water. I just checked, and that same amount of water would cost me $303,689 from my local utility.
I entirely fail to see why Nestle should get a huge discount for water that is then sold to American citizens at $1.79 a gallon, for a 122,976% markup.