Corfu, a colony of Corinth, was engaged at this time in a conflict with its mother-city. Athens assisted Corfu against Corinth, an ally of Sparta. This led to the outbreak of the Peloponnesian War in 431 BC. The fleet of Athens, based in the Piraeus, dominated the naval engagements in the long struggle that followed.

Just as Athens relied on the Delian League, however, so Sparta found support in the alliance which comprised the Peloponnesian League. The Peloponnesian League had superior troops on land, and soon Sparta had Athens under siege. Each spring between 431 and 421 BC, the Spartan army returned to burn down the fields around Athens. The city itself was entrenched behind its city walls and the Long Walls connected to the port in the Piraeus. The siege of Athens left her inhabitants starved and menaced by plague.

In 415 BC, after a six year period of ceasefire, the war spread to Sicily and the southern part of Italy. In a failed expedition, Athens lost large parts of her fleet, giving Sparta the opportunity to strengthen her position in the war. Athens managed to rebuild the fleet and regain some of her former supremacy at sea, but in 405 BC, her dreams were definitively crushed and the entire fleet was once again compromised. Sparta dictated the terms of peace and installed an oligarchy known as The Thirty Tyrants in Athens.

Under the Thirty Tyrants, most of the ship-sheds in the Piraeus and the Long Walls were demolished as part of the disarmament of Athens.