In 1990, the Fukushima Prefecture Marine Recreation Advisory Committee recommended the establishment of a marine culture and learning facility in Iwaki City, and construction of the aquarium began in 1996 and opened in 2000. The nickname "Aquamarine Fukushima" was selected in 1998 from a total of 4,722 applications.

The 2011 Tōhoku earthquake and tsunami on March 11, 2011, caused the aquarium to lose power and a 4.2 meter tsunami hit the building, flooding the entire first floor of the facility. The entire first floor of the facility was submerged. Eighty staff members evacuated to the third floor.

After that, under the direction of Director Yoshitaka Abe, the filtration system, which is a life-support system for captive animals, was operated with its own power generation system.

Many fish died, but some marine mammals and sea birds were subsequently transferred to Kamogawa Sea World, 250 kilometers (155 mi) to the south, Ueno Zoo, Tokyo Sea Life Park, Kamogawa Sea World, Izu Mito Sea Paradise, and Enoshima Aquarium. Although the main building sustained only minor damage, outside pools were washed away, and there was major damage to the electrical system (causing the death of about 90% of the animals in the aquarium).

The cranes used diesel fuel, which is a stockpiled fuel for in-house power generation equipment, for the cranes to carry them out. However, it was difficult to procure fuel and food due to the fact that the northern part of Iwaki City, where they are located, is within the 30 km radius of the Fukushima Daiichi nuclear power plant accident evacuation criteria, in addition to the blockage of the transportation network. The fishing port was paralyzed, and food for about 700 species of marine animals, including seals, crabs, amphibians, and birds, was unavailable. On March 25, it was learned that 200,000 marine animals had been wiped out when the last remaining small generator ran out of fuel and water management became impossible.

The web server in the facility was also damaged by the disaster, causing the official website to be temporarily inoperable, and the official website of Niigata City Aquarium posted the state of damage and other devastation on or around March 16.

The facility was closed after the tsunami, and reopened to the public on 15 July 2011, following restoration.