[4] The sand, mudflats, mangroves and saltmarsh of Te Matuku Bay provides a habitat for eel grass, sea snails, cockles, crabs and worms, including colonies of spiny tubeworm (Pomatoceros caeruleus) that also used to be common in the inner Waitemata Harbour.

[3][5] On the eastern side of the bay are small shell spits, which provide roosting and nesting areas for native and migrating shorebirds.

It provides a habitat for kererū, grey warbler, silvereye, tūī, fantail, kingfisher, and morepork, and are part of the seasonal migration of kākā and shining cuckoo.

[5] The rocky shores and gravel beaches at the entrance to the bay are a habitat for common seashore snails, chitons, acorn barnacles, small black mussels and tubeworms.

[4] The reserve also includes deeper areas off Ōtakawhe Bay at the entrance to Waiheke Channel, where tidal currents expose shell patches that sponges, anemones and soft corals colonise.

People must not feed fish as it disturbs their natural behaviour, and they must take care when anchoring to avoid damaging the sea floor.