http://bugs.winehq.org/show_bug.cgi?id=34674
--- Comment #5 from WineBuG winebugs140@gmail.com --- Okay, I've found on GOG.com forums the person who posted save files with and without the bug. He also confirms the bug affects Linux as well. In his own words:
"I use Linux Mint 14 and I've encountered this issue as well. Oddly enough, when I played this game for the first time earlier this year, water worked fine. But on this, my second playthrough, the recreation pool and the biomass pools have all proven deadly.
Here are the saves: https://web.archive.org/web/20140425212733/http://ubuntuone.com/4HvpZIWXTf3E... [I archived the link]
Save 0 and saves 2-6 are all from my current playthrough and save 1 and saves 7-14 are all from my first playthrough. Save 6 is what needs to be fixed and save 7 (right next to the huge final pool) demonstrates the water being perfectly swimmable. Hope this helps."
From: http://www.gog.com/forum/system_shock_2/system_shock_2_mac_cant_dive/post121