It is easy to find either roller pens or ink for fountain pens that are pigment-based, lightfast and waterproof. It is very easy to test yourself that with such ink water has no effect whatsoever over the written text (after a minute or so of drying after writing). For example, there are many kinds of Uni-Ball roller pens with waterproof ink, but there also many other brands with similar products. (Only fountain pens, roller pens and gel pens may have pigment-based ink, the paste ink used by ball-point pens is easily washed by alcohol or other organic solvents.)
In my experience with graphite on paper, it is a much worse choice, because the writing will fade over the years, due to the rubbing of the paper sheets from each other.
The pigment-based black inks also use carbon, like graphite pencils, but any ink contains not only a pigment, but also a glue that binds the pigment to the paper, so it will not be rubbed out by touching it.
Do you just use regular graphite pencils, like with the HB scale or something?