The walls of the Great Mosque are made of sun-baked mud bricks called ferey, a mud based mortar, and are coated with a mud plaster which gives the building its smooth, sculpted look. The walls are between 16 in and 24 in (0.4 to 0.6 m) thick. The thickness varies depending on the wall's height: taller sections were built thicker because the base has to be wide enough to support the weight. Bundles of palm branches were included in the building to reduce cracking caused by frequent drastic changes in humidity and temperature and to serve as readymade scaffolding for annual repairs. The walls insulate the building from heat during the day and by nightfall have absorbed enough heat to keep the mosque warm through the night. Gutters, made of ceramic pipes, extend from the roofline and direct water drainage from the roof away from the walls. The prayer wall or quibla of the Great Mosque faces east towards Mecca and overlooks the city marketplace. The quibla of the mosque is dominated by three large, box-like minarets jutting out from the main wall and has eighteen buttresses. Each minaret contains a spiral staircase leading to the roof, and on top of each minaret is a cone shaped spire topped with an ostrich egg.

Water damage, in particular flooding, was a major concern of Traoré when he planned the construction. The annual flooding of the Bani River causes Djenné to become an island, and unusually high floods can inundate parts of the city. The Great Mosque was constructed on a raised platform with a surface area of 5625 m² (62,500 ft²), which has so far protected the mosque from even the most severe floods.