Managed to switch from the Padoka PPA to xenial-proposed and thus upgraded to
mesa 18.0.5 and now I don't know if this is just one of the random things with
this game but the problem with water seams to have disappeared for me. I still
get a black (which on some runs are semi-transparant yellow) box where the
sight is and getting hit by the spitter garbles the whole screen but I can now
look at water and swim in it without any problems.