Etrian Odyssey III: The Drowned City is a role-playing game in the Japanese style. The heretofore advanced city of Armoroad has been, for the half of it, submerged by the sea; venturers and wanderers from far and near places come to adventure into the intricate labyrinths lying in the underground to unveil the mystery and reach the mythical Yggdrasil Tree.

The city is where the guild makes preparations and organizes for exploration.

-There is the inn where adventurers can restore health, store and reclaim items and save the game
-The firm wherein to purchase weapons, armours, shields, helmets, gauntlets, accessories and items, forge weapons and change the party's equipment
-The bistro, a meeting-place where to gather information and accept quests from townsfolk
-The explorers guild where new adventurers can be found and members can rest, leave or retire
-The Inver Port, wherefrom to set sail embarking on any kind of sea quest, barter with other gamers
-The Senatus, where the main events of the story take place

Dungeons are travelled across in a first-person view. When foes are engaged in combat, they are displayed on the upper screen, together with small rectangles showing the health and tech points of each of the members of the group. Issued commands are resolved in turns. None of the player's characters is ever displayed. The lower screen permanently displays the labyrinth map: although auto-mapping is a permitted option, manual cartography is a fundamental element of gameplay: by use of the stylus, the player can draw level layouts, while taking note of things found, seen, run into, etc.

The guild may be joined by adventurers of the following classes: prince/princess, gladiator, hoplite, buccaneer, ninja, monk, zodiac, wildling, arbalist, farmer, and possibly some secret others. Each class has an assortment of skills they can learn and master. When a character level goes up one skill point is gained, allowing choice over which skills to develop and to what degree. Every skill is capable of ten degrees of enhancement. A part of the skills have no prerequisites; other ones become available only provided that certain ones have reached a required level. Skill trees are synopsised in a brochure included in the game case. Most weapons can be enhanced in varying ways as well through forging.

It is possible to save the game on no more than a slot; saving points are found in the city and one for several levels only. Registers, namely the Monstrous Codex, Item Compendium, Epic Glossary, give an overview of all discoveries and findings made as well as foes encountered and defeated.