The aquarium is divided into distinct halves with very different stories to tell. The North Building, opened in 2001, follows the theme 'A 3.5-Billion-Year Journey: Animals That Returned to the Sea.' Its exhibits focus on marine mammals -- creatures whose ancestors left the ocean for land millions of years ago, only to return. Here visitors encounter killer whales, beluga whales, bottlenose dolphins, and California sea lions, along with the massive main performance pool where dolphin shows play to packed audiences. The South Building, the original 1992 structure, takes visitors on 'A Journey to Antarctica,' tracing marine life through five ocean regions inspired by the routes of Antarctic research expeditions. Penguins waddle through carefully maintained habitats, deep-sea creatures hover in darkened tanks, loggerhead sea turtles glide through warm water, and coral reef fish flash color across illuminated displays. Together, the two buildings house approximately 500 species.

The aquarium's most dramatic residents have always been its killer whales. In 2011, a male named Bingo and a female named Stella arrived on a five-year loan from Kamogawa Sea World in Chiba Prefecture, transported by ship across Japanese waters. Their daughter Ran 2 arrived by truck the day before. On November 13, 2012, Stella gave birth to a female calf named Lynn -- the first orca ever born at the Port of Nagoya Public Aquarium. Bingo, the largest killer whale ever kept in captivity in Japan, died on August 2, 2014 after an illness. Since then, the aquarium's orca family has consisted entirely of Stella's descendants. Stella herself eventually moved to Kobe Suma Sea World in March 2024. Her grandson Earth, born at the aquarium on October 13, 2008, became one of the facility's most popular residents, but died of gastric torsion on August 3, 2025 at age 16. As of late 2025, only Lynn remains at Nagoya -- the sole killer whale at the facility. The aquarium weighs its orcas four times a month and adjusts their diet accordingly -- a detail that speaks to the intensive care these animals require.

The Port of Nagoya Public Aquarium has earned multiple breeding awards and Koga awards from the Japanese Association of Zoos and Aquariums for its work with species that are notoriously difficult to raise in captivity. In 1995, the aquarium achieved the first successful artificial hatching of loggerhead sea turtles from an indoor spawning ground anywhere in Japan -- and then went further, breeding loggerheads successfully for two consecutive generations. The penguin breeding research facility has produced its own string of successes, including the hatching of emperor penguins, among the most challenging penguin species to breed outside Antarctica. In total, the aquarium has received breeding and conservation awards for 18 different Antarctic and marine species, establishing Nagoya as one of the most productive aquarium research programs in the country.

The aquarium sits in the Minato-ku port district of Nagoya, a short walk from Nagoyako Station on the Meiko Line subway. The surrounding area, known as the Garden Pier, was reimagined around the aquarium's presence, turning a working port into an attraction that draws visitors year-round. Beside the aquarium, the retired icebreaker Fuji -- the orange-hulled research vessel that made 18 voyages to Antarctica between 1965 and 1983 -- is permanently moored and open as a museum ship. The pairing is deliberate: the Fuji's Antarctic expeditions inspired the South Building's thematic journey through the five oceans. For the aquarium itself, accredited as a museum-equivalent facility under Japan's Museum Act, the waterfront location is more than scenic. That direct pipeline to Nagoya Harbor's seawater gives its tanks a living connection to the Pacific, a reminder that the creatures inside these walls have relatives swimming in the currents just beyond the breakwater.