The species exhibited include harbor and northern fur seals, California sea lions, African and southern rockhopper penguins, giant Pacific octopuses, weedy seadragons, and thousands of saltwater and freshwater fishes.

[5] As part of the city’s goal of revitalizing the waterfront, a new, modern aquarium, designed by Peter Chermayeff of Cambridge Seven Associates, was planned starting in 1962.

[8] As the aquarium’s location on the wharf limited its ability to expand, Discovery served as a floating addition containing a 1,000-seat amphitheater overlooking a 116,000-US-gallon (440,000 L) saltwater pool for marine mammals.

[10] Also in 2020, contemporary artist Shepard Fairley designed and painted the mural A Vital and Vibrant Ocean for All, featuring a North Atlantic right whale, on the façade of the theatre.

This open-air exhibit lets guests and passersby view the aquarium's California sea lions and northern fur seals.

The 23,000-square-foot (2,100 m2) off-site facility, located in Quincy, has large tanks for holding animals during exhibit renovations, quarantining new arrivals, and rehabilitating rescued sea turtles.

In 2011, the aquarium added an Australian Great Southern Reef exhibit, featuring leafy and weedy seadragons, to the Temperate Gallery and started its own captive breeding program for the species.

[12] In the last of $42 million in upgrades that started in 2007, the aquarium once again worked with Cambridge Seven Associates to make improvements to the Giant Ocean Tank, including an expanded coral reef, larger, acrylic viewing windows, and a more advanced lighting array.

Open and accessible for viewing at the top, the concrete tank is surrounded by a spiral walkway that allows guests to see into the exhibit from every angle through 67 acrylic windows.

The New Balance Foundation Marine Mammal Center on the rear of the building can also be viewed from the outside (from the Harborwalk), and is home to a small colony of three California sea lions and one northern fur seal.

The base of the Giant Ocean Tank sits in a 150,000-US-gallon (570,000 L) tray of saltwater containing a habitat for penguins, including Africans and southern rockhoppers.

Four levels of smaller exhibits, open to the atrium and accessible via either the spiral or a separate series of ramps, surround the Giant Ocean Tank and penguin habitat.

The aquarium has advocated for action on climate change, sustainable fishing practices, and marine animal conservation at the city, state, and federal level.

In the 1970s and 80s, the aquarium and numerous other local organizations called for the cleanup of Boston Harbor and the Charles River to make it safe for fishing and swimming, which was ultimately successful.

In 1988, the aquarium announced its plans to sell the Central Wharf property and build a larger facility across the Charles River at the Charlestown Navy Yard.

Flooding Drydock 5 at the Navy Yard would create an exhibit of unprecedented size for dolphins and pilot whales, with underwater viewing tunnels as deep as 19 feet (5.8 m) below ground level.