Modern Nuclear-powered & Diesel-Electric submarines are only limited by crew limitations, specifically food and other supplies. Without the need to replenish food, they can stay submerged indefinitely since oxygen is generated, carbon monoxide and dioxide is filtered, and potable water is distilled. However, DE submarines are also limited in range and time at sea by available fuel, while a Nuclear Powered boat doesn't have that problem.
My own personal longest submergence period is 72 days, though others have exceeded that limit. The Seahorse (SSN-669) during her circumnavigation of the globe in the 1982, spent over 180 total combined days submerged; they had only 2 ports of call during the entire mission, and they only lasted a few days each. The USS Parche (SSN-683) a Submarine Development boat, usually had the most submerged time in the submarine fleet, since her extreme classified missions did not allow her to make any Ports of Call. Her typical deployments were about 3-4 months, virtually all of that time submerged save for port exit and entrance.
After about 2 months, depending on what the mission is and whether or not the boat has been able to snorkel (and thus bring in fresh outside air), the crew starts getting a bit snappy and short tempered, and the air starts getting a bit stale if it hasn't been changed out. Filtered air is okay, but it gets old after a while. Other things like fruit and fresh vegetables are also a big deal, as well as fresh milk, since they're the first food items to get used after getting underway for a long mission. Long deployments also mean that most of the crew's complement is onboard, as well as any civilian riders required. That means it's a lot more cramped than usual. Hot bunking (3 crewmen sharing 2 bunks - 2 sleep while one is on watch) is common during long deployments, though typically assigned to junior crew members.
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