Sewer Sam begins with Sam waiting in Central Park to meet his girlfriend Sally, but he gets swept away by the sewer system. He finds himself trapped and must navigate through the sewers to find a way out. The main objective is to destroy the Russian submarines that have blocked off the system.
The gameplay involves navigating through different types of tunnels, including those with solid floors, water passages, and pits. Sam can move quickly on dry land but must be careful in water as it slows him down. He can also use the water canals to his advantage by shooting at the Russian submarines located within them.