Thucydides' full description of the harbor at Pylos is part of his discussion of the Spartan strategy for thecampaign (iv 8).
. . . and the Lacedaimonians . . . expected the Attic fleet from Zacynthos to come to the rescue and intended, if they had not captured Pylos by that time, to block up the entrances to the harbor, so that the Athenians could not sail in and use it as an anchorage. (The island called Sphacteria extends alongside the harbor, and lies close to it: hence the anchorage is safe and the entrances narrow–the entrance by Pylos and the Athenian fortifications giving a passage for two ships through the channel, and the entrance by the mainland on the other side a passage for eight or nine . . . ) These entrances then, they intended to block up tightly with ships lying parallel to each other, prows to the enemy: and since they were frightened that the Athenians might use Sphacteria as a military base, they ferried hoplites across to it, and stationed others along the mainland. By this plan, they thought, the Athenians would find both the island to be enemy-occupied and the mainland, which gave them no chance of landing (for the coast of Pylos itself, outside the entrance and towards the open sea, is harborless, and would give them no base of operations to help their troops): and equally they themselves would probably be able to capture the place by siege, without a sea-battle or any unnecessary danger–there was no food in it, and it had not been properly prepared for a siege. This, then, was their agreed plan . . .
Although one would think this a clear and detailed geographic description, historians have not yet found a location at Pylos for the harbor which satisfactorily matches it.