It depends on what the job consists of. Pile foundations may or may not be influenced one way or the other depending on what is to be built. It also depends on the soil type encountered. You should inquire of the drillers and see what they really observed. A quick job of get ind get out may not give the water any time to be entering the bore hole.
For a simple bridge job with one span, it may not mean anything. For a multi- span job with piers in the water, it means something different, mainly for construction. For a building construction job it means something quite different yet.
Also, even though it may be near water, with rather tight soil and a water supply well nearby, that may explain it.
In other words, you don't say enough for anyone to properly help you.