The player uses a submarine to shoot at enemies and rescue divers. Enemies include sharks and submarines, which shoot missiles at the player's submarine .[3] The player must ward off the enemies by firing an unlimited supply of missiles while trying to rescue divers swimming through the water. The points awarded to the player for shooting an enemy starts at 10 points each, and increases as the game advances. The sub can hold up to six divers at a time. Each time the player resurfaces prior to having a full load of six divers, one of the divers is removed.
The submarine has a limited amount of oxygen. The player must surface often in order to replenish the oxygen, but if the player resurfaces without any rescued divers, they will lose a life. If the player resurfaces with the maximum amount of divers, they will gain bonus points for the sub's remaining oxygen. Each time the player surfaces, the game's difficulty increases; enemies increase in number and speed. Eventually an enemy sub begins patrolling the surface, leaving the player without a safe haven.
The player starts the game with 3 extra lives, and is awarded an additional extra life each time the player scores 10,000 points.
Seaquest can be played single-player or with two players alternating turns.