The problem is that while reservoirs can be refilled from the surface watershed with a good rainy season or two, aquifers take decades of water slowly percolating down through the soil to replenish. If your rate of consumption exceeds the refill rate, well, you're in a bit of an unsustainable situation and the clock starts ticking.
As the drought progressed and surface water became scarce, agriculture started drilling deeper and deeper wells to access the aquifer reserves. The aquifers got so drained that there were stories of fracking companies being hired to drill wells which had depths beyond the capabilities of most traditional well-drilling machines.
Worse, there's also positive feedback loops at play -- as an aquifer gets depleted, the ground above it can settle in a way that slows the refill rate (I've heard it described as the volume occupied by the water goes away so dirt fills in the small gaps creating more compacted/sealed off soil). If the refill rate slows down and your consumption rate stays steady or increases (development!), well, the aquifer's rate of depletion accelerates. Feedback is a bitch.
The anecdote about fracking companies being called in to drill super-deep water wells tells you all you need to know about how market forces price the sustainable consumption of our water reserves.