The building where the aquarium is located was built initially as a natatorium in the 1920s, an indoor saltwater public bath, with the water pumped from the Pacific Ocean through a pipe still visible today at the tide line, and then heated. It featured balconies where people could watch others swim in the pool below. A decade later, the Great Depression broke its economic feasibility. The building later served as a salmon rearing facility, and then a place to watch wrestling matches. The aquarium was founded in 1937, making it one of the oldest in the United States. It uses the same pipe that was installed in the 1920s to fill the aquarium tanks.
During March 2013, a boat lost during the 2011 Tōhoku earthquake and tsunami drifted across the Pacific Ocean and washed up on the shores of Washington carrying trapped live fish. The so-called Tsunami fish was put on display at the Seaside Aquarium.