If you look up the Isonzo front, they dug trenches and whole caverns even at elevations (up to 3900 meters) where there is nothing but stone on the ground.

Look at http://foto.sta.si/en/#!a/68446/776563 to get an idea of the terrain.

Note that most trenches (all but the one closest to the enemy positions) would not be dug while exposed to direct fire (artillery could still reach them).

There were not just two opposing parallel trenches all along the front. Each side had a whole system of trenches, several rows laid along the front, with other trenches connecting them.

Some of the trenches (where possible) were even dug by mechanization.

If the new trench position were under direct fire, soldiers would first pile up dirt or stones for initial cover, and then dig behind it.

Also note that bullets zinging overhead are a great motivator for digging, and a hole that would be too much trouble to a civilian with a pick would be lovingly deepened by a soldier who would have to trust his life to it.

All in all, I think that WWI soldiers would prefer a trench in a stony area to one in an area with a high ground water level. It is more work to dig in a stony area, but in a high ground water area, you can NOT dig any deeper, and your trench will have water in it, leading to trench foot and even drowning.

See http://ww1centenary.oucs.ox.ac.uk/body-and-mind/slimescapes/ for instance.