Wouldn’t leaks from underground pipes end up back in the aquifer and not really be a net water loss in the long term?

Water in the ground from leaky pipes will travel in all directions. Some of it may end up back in the aquifer, but some will end up on the surface and evaporate. Depends on conditions near the pipe and the volume of the leak.

Texas state laws make regulating groundwater use very difficult. The Trinity aquifer is probably going to go dry in ten years.