In July 2003, the Water Cube design was chosen from 10 proposals in an international architectural competition for the aquatic center project.The Water Cube was specially designed and built by a consortium made up of PTW Architects, the engineering firm Arup, CSCEC (China State Construction Engineering Corporation), and CCDI (China Construction Design International) of Shanghai. The Water Cube's design was initiated by a team effort: the Chinese partners felt a square was more symbolic to Chinese culture and its relationship to the Bird's Nest stadium, while the Sydney based partners came up with the idea of covering the 'cube' with bubbles, symbolising water. Contextually the cube symbolises earth whilst the circle (represented by the stadium) represents heaven. Hence symbolically the water cube references Chinese symbolic architecture.

Comprising a steel space frame, it is the largest ETFE clad structure in the world with over 100,000 m2 of ETFE pillows that are only 0.2 mm in total thickness. The ETFE cladding allows more light and heat penetration than traditional glass, resulting in a 30% decrease in energy costs.

The outer wall is based on the Weaire-Phelan structure, a structure devised from the natural formation of bubbles in soap lather.The complex Weaire-Phelan pattern was developed by slicing through bubbles in soap foam, resulting in more irregular, organic patterns than foam bubble structures proposed earlier by the scientist Kelvin. Using the Weaire-Phelan geometry, the Water Cube's exterior cladding is made of 4,000 ETFE bubbles, some as large as 9.14 metres across, with seven different sizes for the roof and 15 for the walls.

The structure had a capacity of 17,000 during the Beijing Olympic Games that is being reduced to 7,000. It also has a total land surface of 65,000 square meters and will cover a total of 32,000 square metres. Although called the Water Cube, the aquatic center is really a rectangular box (cuboid)- 178 metres square and 31 metres high.