On the main beach of Ōtata Island is a large, historic midden. Sadly, meters of the midden were lost in a large storm in January 2018. The midden provides archeological evidence which can sit alongside the oral histories of mana whenua and the Neureuter family.

The Hauraki Gulf is home to a threatened population of Spotted Shags, thought to be genetically distinct. Whilst the Spotted Shag is relatively common in other parts of the country, in the Hauraki Gulf the birds are now limited to just two colonies, on Tarahiki and Waiheke Islands, with an estimated population of 300 breeding pairs.

Geckos are an important component of native ecosystems both as predator and prey, and play a role in plant pollination and seed dispersal. The gecko population from The Noises has been used as a source population for translocations to other islands within the Hauraki Gulf.

Many marine animals rely on making sound and listening for sound queues as a matter of survival. The University of Auckland have placed a camera on Ōtata Island and a hydrophone in the bay to gather data to determine the impact recreational boat noise is having on the reef systems around The Noises.

Seabirds of The Noises have been studied for many years. In November 2019, Auckland Council commenced a 10-year study of the takahikare/white-faced storm petrels, pakaha/fluttering shearwaters, kuaka/northern diving petrels, oi/grey-faced storm petrels and korora/little blue penguin on Ruapuke/Maria Island.