There’s weather underground. I know that’s a weird thing to say, but in a sense, it’s true. As a matter of fact, there’s a whole underground water cycle, with precipitation, lakes, seas, and rivers. And the majority of the world’s fresh water is caught up in that cycle. Let me explain.
Most soils contain a fraction empty space, even dense soils like silts and clays. And most soils are, to a lesser or greater degree, water-permeable.
Surface water (rainwater, lakes, rivers, etc.) takes the place of clouds. Water from the surface seeps down into the soil like slow-motion rain. How fast this water descends depends on how permeable the soil and rock are. Eventually, this groundwater encounters a completely impermeable surface, be it dense clay, thick limestone, or solid bedrock. Then, as water tends to do, the water pools. It doesn’t quite pool in the traditional sense. Apart from in caves, there aren’t a lot of underground lakes: the pools of water exist in the pores and cracks in the ground. The surface of these underground pools of water (the “water table”) is defined by the point where all the spaces are full. And though it’s definitely not a traditional water surface, it behaves a lot like one: the water table tries to reach equilibrium under gravity and flatten out.
But because of the drag provided by the surfaces of all those tiny pores, groundwater flows pretty slowly. Imagine replacing a six-inch pipe with a six-inch bundle of coffee stirrers: they might have the same total cross-section, but capillary drag means the coffee stirrers are going to resist the flow a lot more. So groundwater behaves like a very thick, viscous liquid. Sometimes, it can take thousands of years to flow from one point to another. And this leads to problems.
Water has weight. Quite a lot of it, actually: every gallon weighs 8.3 pounds. A body of water exerts a lot of pressure. That’s true of groundwater, too: the weight of a pool of groundwater, along with the weight of the overlying rock and soil, puts the soil pores under pressure. This pressure is helpful. When a person drills a well, that well fills up with water, usually to the height of the water table. When the water is pumped out, pore pressure forces water out of the walls of the hole and refills it.
Sometimes, you don’t even need a pump. Imagine, if you will, a long slope. The ground’s surface is pretty much impermeable to water. Below that is a permeable layer, and below that, another impermeable layer. Now, say that, at a higher altitude (up in the mountains, perhaps), that top impermeable layer disappears. Water enters the soil there and flows down-slope through the permeable layer until it inevitably fills that layer up. If you drill a well near the bottom of the slope, where the pressure is high, you might end up with an artesian well: the equivalent height of the water table is actually above the surface, not below. The water spews out on its own, under pressure. You might not even need a pump.
Humans need fresh water for pretty much everything. We (and our livestock) can’t drink salt water. Crops can’t tolerate salt water. Agriculture (which is one of the pillars of civilization) wouldn’t be possible without freshwater irrigation. This all presents a problem: Earth is covered in water, but the vast majority of that is salty seawater: 96.5%. That only leaves 3.5% freshwater. Of that, 68.7% is frozen in glaciers and ice-caps. Surface water only makes up 1.2% of the freshwater, and over two-thirds of surface water is trapped as permafrost. Groundwater makes up 30.1% of the freshwater, and it’s the only source that’s easy to extract.  After all, all you have to do is dig a well.
For many thousands of years, there was nothing to worry about. A good well could provide water for a whole village or a whole farm. Now, though, with our population booming, the groundwater supply is under stress. The Ogallala Aquifer is an enormous underground sea (of sorts) buried under the American Midwest. By some estimates, it supplies irrigation water for 30% of U.S. agriculture.  Wells have been drilled into the Ogallala for a long time. But now, in the era of high-intensity industrial farming, there are places where we’re pumping from the aquifer faster than it can refill. And groundwater moves slowly, so when a well pumps water out, it takes a while for more water to flow in and replace it. If the pumping rate is fast enough, it creates a divot in the surface of the water table, called a drawdown cone. If there are too many wells too close together, or a few very large wells, these depressions can add up, dropping the water table low enough that shallower wells go dry. What’s more, with groundwater now flowing towards the low spot, the flow patterns change. If there is, for example, a leaking underground storage tank or sewer or oil well, contaminants will flow towards the wells, dragging plumes of contamination through the ground.
But perhaps a more serious consequence of the overuse of groundwater is subsidence. As I said before, a column of water (ground or otherwise) produces pressure. Quite a lot of pressure, as it turns out. The ancient Romans mined using a method called ruina montium: when rocks contained gold that was too deep to mine, they would dig narrow shafts down behind the rock face, then fill those shafts with water. The pressure of the water blew out the rock face, reducing it to rubble and allowing the gold to be sifted out.
A similar process is at work underground: pore pressure presses on everything. But if enough groundwater is removed, the pore pressure falls. In some cases, when the pressure is removed, the water-bearing rocks collapse (the severity depending on the type of rock.) At this point, even if the groundwater is replaced, the ground has permanently lost some of its water capacity. This collapse of dry aquifers is called subsidence. In some places in California, the effect is quite dramatic, with the ground subsiding as much as ten or twenty or thirty feet.  The problem is especially visible in places like California, Florida, and Mexico, since these places are hot and largely irrigation-dependent, and because the local geography favors subsidence. Florida, for instance, is plagued by sinkholes.
The population keeps growing and growing. Not so long ago, our population surpassed seven billion. And all seven-billion-plus of us need water, and need food produced using water. Groundwater is an attractive source, especially in dry, landlocked parts of the world. But groundwater is also the kind of natural resource that’s easy to neglect or abuse. After all, it’s invisible, and because it moves slowly, the effects of over-use take a while to manifest. And as with so many natural resources, we’re entering an era where we can’t afford to take it for granted. We need to watch our consumption, and we need to minimize waste. Then again, that goes for pretty much all of our resources.