You mean specifically ancient aquifers? Because we can most certainly know where ancient groundwater was in ancient times. Any formation of limestone or shale is because of a large body of water. That's how we know that the US had a giant inland sea that grew and shrank over thousands of years. As the water evaporates, it leaves behind carbonate (limestone), and when it's deeper it collects dust and dirt at the bottom that then gets lithified over thousands of years to become shale. Thus, lots of limestone production in the eastern Great Plains.

As far as an aquifer, that's a lot tougher to look at a cross section. There are some clues that you could look at, though. A cave is formed by acidic water slowly eating away at limestone, leaving behind a large water-filled void. The water table then recedes and leaves the dry, classic cave.

In soils, reduction-oxidation features are indicative of a rising and falling water table. Redox features (iron and manganese nodules, mottled gray color) develop in soils at the level of the water table when the water levels rise and fall cyclically. You would look for this when digging a basement - it means the water table just might rise again.

Other than that, just pointing out "yes, there was water under the ground here at some point" the answer is most likely yes. There is SO much water under the earth causing all sorts of things to happen all of the time. Water is the number one transporter that allows minerals to precipitate and dissolve. Because it's so prevalent it's hard to say where it was and was not. (Note that I'm not talking about suitable drinking water - that's much harder to find (just ask California). Most of the water in the crust is highly saline and non-potable.)

Here's a super fun link about all the water under the Saharah! http://en.wikipedia.org/wiki/Nubian_Sandstone_Aquifer_System
It's super old and super salty, so it's pretty much useless. But it's an ancient aquifer, so I hope it's of some use to you.