A well can allow oxygen into the soil where it will thin out any organic materials present, possibly causing subsidence. Without redigging the well using expensive methods it is hard to prevent this. Also, if the water is in a reservoir of some kind, reduction of that reservoir can cause subsidence. There is not much you can do about either of these problems except trying to locate the well elsewhere maybe.
The most common leaks that don't show themselves (damage, or water on the ground) are either inside toilets (the toilet leaks water from the tank to the bowl) or in the water line outside the house.
Right where the water line comes into the house there should be a valve. The first place I would start is to turn off the main valve in the house then check the meter. Leave it for a few hours and check it again. If the meter has turned then the leak is underground and it will be a pain to fix. I've heard that if you do confirm that that's the problem, some professionals have an expensive tool to find such leaks. If you don't have a valve right where the water enters the house I would seriously consider starting by adding one in (or have a plumber do it).
If that's not the problem I would put a bunch of food coloring in the tanks of all the toilets (not the bowls) and check in a while to see if the color has leaked down into the toilet bowls. If any of the toilet bowls do have color in them, that right there is a leak that doesn't cause any damage, but does waste water.
Some water heaters can absorb some water into the insulation, making it less obvious that it's leaking but once the insulation is saturated, that wouldn't really make a difference.
Other than that, watch carefully for any signs of water or water damage near the base of all of your walls, on all of your floors (especially near the walls), and in all of your ceilings. Regularly check all around your water heater (especially around the unions, T&P valve, valves, and the base).
If you don't find anything I would seriously consider getting a plumber (especially if you know one) because water damage can be very costly. Not being a plumber myself, I don't really know how much they can do to track a leak but I'm sure they would know more than a DIYer like me.
I hope this helps.
Best Answer
Assuming you have a shallow well pump. I would start looking from the pump to your well. This is where you will get air sucked into the water without having a water leak. Tighten all the hose clamps, you may need to add thread sealant to primer plug or any threaded fittings.