The lack of invasive predators, intact native forest, and large numbers of breeding seabirds give the Noises significant conservation value.

[1][2] ha m The islands are composed of complexly folded Jurassic greywackes and argillites,[3] with rocky indented shorelines and wave-cut platforms that expose up to 25 m of rock at low tide.

[18] Their lack of invasive mammals and low weed numbers make them important from a conservation point of view, and they are a seed source for regeneration projects on other islands.

[19] It is dominated by pōhutukawa (Metrosideros excelsa), red matipo (Myrsine australis), coastal karamu (Coprosma macrocarpa), karo (Pittosporum crassifolium), houpara (Pseudopanax lessonii) and māhoe (Melicytus ramiflorus).

[1] Motuhoropapa has a more mature forest with a canopy averaging 6–10 m high and reaching 20 m. Similar to Ōtata's, it contains pōhutukawa, karo, houpara, māhoe, and coastal karamu, but also includes wharangi (Melicope ternata), with kohekohe (Dysoxylum spectabile) in the understorey.

Clearing the summit in the 1950s to build the safety light may have allowed the establishment of invasive weeds, notably the vine Dipogon lignosus, known as "mile-a-minute".

[2]Thirty two species of land birds are present, thirteen breeding there, including fantails (Rhipidura fuliginosa), silvereyes (Zosterops lateralis), tūi, bellbird and grey warblers (Gerygone igata).

[2] Spotted shags or kawau tikitiki (Stictocarbo punctatus) were common in the Hauraki Gulf as recently as 1910, but fishermen at the time regarded them as competitors for their catch, and they were widely persecuted and shot for sport.

This corresponded with illegal shooting of birds in the colony, increasing boating and fishing around the islands, and dramatic declines in populations of pilchards and anchovies in the Gulf.

[1] Norway rats (Rattus norvegicus) began to arrive in the 1950s, either swimming from garbage dumped from a ship or stowing away on boats travelling to Ōtata and Maria Islands.

[1] The effects of rats were first noted in late 1959, when they were found to be killing chicks of white-faced storm petrels on Maria Island and David Rocks.

Hundreds of dead petrels were discovered by Waiheke schoolteacher Alistair McDonald, who with his class formed a junior division of Forest and Bird, and in January 1960 wrote to the Department of Internal Affairs requesting £5 to purchase warfarin rat poison.

Twice in 1960 poison baits were laid by Junior Forest and Bird, and the campaign was continued by Don Merton of the New Zealand Wildlife Service until September 1963.

[35]The soft seafloor around the Noises is notable for the presence of rhodoliths or coralline algae, as well as dog cockles (Tucetona laticostata), whose accumulated mounds of thick shells are colonised by encrusting and free-living invertebrates.

[19] The scallop beds have been extensively dredged and harvested by divers, and much of the sea-floor habitat has been destroyed, leading to a decline in horse mussels (Atrina zelandica), sponges, and rhodoliths.

[16][37] Extensive fishing has led to the decline of snapper and the almost complete disappearance of koura or spiny rock lobsters (Jasus edwardsii) in the Hauraki Gulf.

[16] The Neureuter family have observed over several generations a decline in marine life at Ōtata, including the disappearance of baitfish, squid, and koura, and the decrease in size and abundance of snapper, trevally, kingfish and kahawai (Arripis trutta).