This game just moved up in my "to play soon" list.
Hey, make sure to at least try it on the hardest difficulty.
n00b! Save the damn bullets, and use stealth when possible. Do not shoot things unless you really need to. I did it on the hardest difficulty, it is very possible. When you get to the toxic bubbles, note their spawn locations, these can be destroyed with a few bullets.
Also, time your movement. Your ally's movement will spawn one round of bubbles, and your movement will spawn another. Make sure to give him some room for him to go ahead first, that way it will be a lot easier to deal with one round of bubbles, instead of two.
Also x2, when you get to the metal room near the end of this section, just run and shoot the crap out of those bubbles following you, because once you're past the metal door, they won't spawn anymore from their spawn locations, and only you will have to deal with those already spawned.
I'm not really good at shooters, but that game didn't really was that frustrating for me. Maybe you are missing something that makes it more doable? I don't recall the section you are describing, it's to long since I played it. No help there, sorry.
That one is near the end, when you get inside the nuclear facility. Just before you use the crane to kill the 'boss', if that creature can be called that way.