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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: bit.ly/1dPKqOU

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.

Edit: I said earlier this year, I actually meant early last year
Post edited January 21, 2014 by EdgyTryhard
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EdgyTryhard: I use Linux Mint 14 and I've encountered this issue as well.

...
Finally, someone has confirmed the issue on Linux as well! Thank you!

IF SOMEBODY FINDS THE EXACT THING CAUSING THE WATER BUG TO APPEAR, attach your Wine debugging log and Wine debug trace to this System Shock 2 bug report. Without these logs, Wine developers wouldn't be able to fix it (or it'll be much harder to do).
Post edited January 21, 2014 by zU84ha76la
done: sendspace.com/file/92spmt
Could you please help me?
www.sendspace.com/file/7g0kxz
yeah: sendspace.com/file/0ykmle
Thank you very much!
I'm having the same issue as others.. how are these saves being "fixed"?

sendspace.com/file/osidyw
the save is unusable, it should a have a couple of megabytes, not 200kb. try making a new one.

the fix is actually not all that difficult - you need to have the Shocked editor set up properly, load the save via the editor exe, switch to the editor mode, locate the player, and edit his air supply value (negative values are bad, 0 is good). then you return to the game mode, save, and it's done. sometimes the saves are extra corrupted, if that happens, the value needs to be modified via loading a dml patch - that's why it's almost useless to try to create some automatic patch tool.
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voodoo47: the save is unusable, it should a have a couple of megabytes, not 200kb. try making a new one.

the fix is actually not all that difficult - you need to have the Shocked editor set up properly, load the save via the editor exe, switch to the editor mode, locate the player, and edit his air supply value (negative values are bad, 0 is good). then you return to the game mode, save, and it's done. sometimes the saves are extra corrupted, if that happens, the value needs to be modified via loading a dml patch - that's why it's almost useless to try to create some automatic patch tool.
ahhh... it's been a long time since I messed around with any game editors. Thanks for helping all of us with the saves!

um, here's a new link :)

sendspace.com/file/l06fd5
sendspace.com/file/akpwix

this one was a level2, extra corrupted.
can someone help me with mine please :(?
I tried downloading ShockEd but I can't run it on my mac, so its useless.

sendspace.com/file/4dtorb

I don't know how corrupted my save might be :/
http://www.sendspace.com/file/gt9jfx
works like a charm :) thanks for the help, and the super speedy fix!
I'm not sure if this has been mentioned before but I found a work around for this bug.

It may be useful for people who are too scared to ask for help (like me :)) or don't know how to upload things.

I tried diving in the water in the alien and I died and game over. I then loaded a save from just before I went in there, ran back to the Von Braun, level 5 and jumped in the pool. I died, but I was brought back to life at the Bio Reconstruction Machine. I then went for a swim in the pool, swam around no problems.

It seems that the drowning reset the bug.

I then ran back to the Rickenbacker, headed into the alien and had no problem swimming after that. Managed to finish the game last night (for the first time in my life). Thoroughly enjoyed it and highly recommend everyone try it out.
this is an interesting, and very usable workaround. thanks for the info.

//anyway, I'll have to make it irrelevant - found a permanent fix. download this dml file, drop it into your SS2 folder, and the problem will be solved (even saves which are already corrupted will become usable again).

I will submit this to the GOG team after some testing, so the next (mac) update should fix this for good.
Post edited March 29, 2014 by voodoo47