Robert House said:
1. What are the psychological effects on staying inside of a submarine, submerged underwater for months? Is there any sort of cabin fever?
2. How did your submarines prevent CO2 from building up?
3. Was there ever any trouble with marine life? (Sharks, squids, jellyfish)
#1 Psychological effects? Pretty much as expected. When you're on a boomer, which are the ones that stay submerged a long time, you're on a semi-regular schedule. You know you're on patrol for approximately x days and then back on shore for off crew while the other crew (blue and gold crews on each boat) has it out on patrol..
Also when you get qualified in submarines (get your dolphins, which is about the same as a pilot getting their wings) the certificate says "Having proved himself under stress..." If there are sailors you don't trust your life with, you intentionally inflict stress on them until you're either comfortable that they can handle it, or until they break and end up on a surface ship. When there is a fire in a garbage can, that's your oxygen burning, you can't have someone around who will panic or run away.
We broke one guy, he was a compulsive liar, including lying about performing periodic maintenance on survival equipment. As part of normal periodic training/exercise they shoot "water slugs" out the torpedo tubes, basically just cycle all the mechanisms and then drain the tube without actually loading a torpedo in it. Afterwards they have to dry the inside of the tube. He was volunteered to do it (as non-qualified sailors often get "volunteered" for dirty tasks) and while he was in the tube they closed the breech door. We could hear him screaming on the sonar array. He volunteered himself off the boat as soon as we got back.
Two guys broke on their own, one was a very religious type who ended up making gibbering noises and had to be taken off, the other just decided he was leaving in mid patrol, just packed his sea bag and started climbing the forward ladder saying he was going home (we were several hundred feet down at the time)
#2 Amine solution in the CO2 scrubbers. There was a CO burner, CO2 scrubbers, and oxygen generators, 2500A of DC current passed through seawater will make a fair bit of oxygen. There was a pump to discharge the hydrogen overboard. Initially they let it all out through a small pipe but then discovered that the hydrogen wake could be tracked from satellites under certain conditions, so they added diffusers.
The reactor is one of the least scary things on the boat. You have flasks of pure hydrogen to "patch up" the water around the reactor (not a physics guy, I know the zoomies knock bits loose and they have to put hydrogen back into make it go) which are pretty scary, and the gigantic oxygen generators with extremely high electrical currents and pure oxgygen in them. Then there are the huge banks of lead acid batteries down below all generating hydrogen gas as they get charged...there are some shipyard photos of one boat that was still being constructed when someone sparked in the battery compartment. Two decks worth of equipment and people was a 12" veneer stuck to the top of the pressure hull.
#3 Sea life... depends on what you call problems. They make it hard to see where you're going.
Snapping shrimp are frequent cause of problems, they like the thermal wake from the reactor and when you're on patrol you're just moving 3 to 5 kts so they can keep up. for a long time. They sound exactly like bacon in a frying pan when you're listening on the stack (most sonar is visual, just looking at digital or paper displays, but there are still important/critical cues that require listening)
Sometimes sperm whales would discover the shrimp. They clop their jaw when they're eating shrimp. They're called "carpenter fish" because it sounds exactly like a gang of carpenters framing a house, sometimes the hammers happen to hit in sync, mostly they're random, but they're constantly banging. If they don't go away pretty quickly the boat has to go deep or speed up or both to shake them off. You can't hear well with all that banging going on, and you really don't want to deploy a towed array sonar while there are great big critters out there who might want to rub/scratch on it..
Sometimes dolphins or pilot whales will visit and surf the pressure wave on the bow, but not very often (in the north Atlantic at least)
Algae are probably the most problematic. Since the boats move very slowly on patrol, algae can turn the hull bright green if you're in warm water. That bright color can be seen quite a ways down by aircraft flying overhead.
There's a story (apocryphal?) that during WWII the British submarine captains would surface and feed stale bread to the seagulls. Every time the seagulls saw a big dark shape in the water they'd congregate over it waiting for dinner. If the shore batteries knew there weren't any British submarines patrolling that stretch of shoreline and there was a big crowd of seagulls, they'd open up and shell the crap out of whatever it was the seagulls were seeing. If the story is true I imagine there were a few briefly surprised Germans betrayed by the seagulls.
) 
) My point was basically that the ocean seems to have this constant motion in any location and that storm affects are only around 30 or 40 meters below surface, as far as I know.