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The aquarium, which is a star attraction of the zoo, consists freshwater, marine and brackish water sections. It was established for 40 years.

Many fish species and corals, mollusks, echinoderms and arthropods are in 22 tanks.Visitors could observation most behavior patterns of these aquatic organisms such as breeding, colonization, symbiosis and competition etc., from outside the tank.

There are 50 fish species identified as endemic to Sri Lanka. Out of them many different varieties are exhibited in the aquarium. Very rare varieties of fish including endemics have been bred in the aquarium and in zoo ponds as well.

An Amphibian section has been opened in side the aquarium to make aware the public on Amphibians.

Currently there are three tanks with Amphibians, where as six species are living in their near natural conditions. Endemic frog species Polypedates cruciger is among the six Amphibian species.