Mangarakau is home to a wide variety of plants, ranging from terrestrial trees to aquatic plants. The growing list of plant species includes over 30 species of orchids. Colonisation by introduced plants is kept in check by the Friends of Mangarakau members.
The reserve is fortunate to have few noxious or invasive weeds other than gorse, blackberry and some exotic tree species but these require constant work to keep them from re-establishing. While unpleasant, gorse can be a useful nurse crop for developing forests but is a nuisance where open wetland is desirable. Vigilance is required to prevent seeds of other pest species coming in on spades, boots and road maintenance equipment.
Tree planting and active restoration has been done using local seed grown off site and transplanted.
The swamp abounds with frogs and fish, including eels, banded and giant kokopu, inanga, koura, freshwater shrimp and Nelson Marlborough's only species of brown mudfish.
The part of the Whanganui Inlet which links to Mangarakau Swamp is a marine reserve and harbors 163 different estuarine invertebrates, more than in any other South Island estuary.
Fernbird, grey warbler, tom tit, brown creeper, robin, bittern, marsh crake and spotless crake all use and live in the swamp.
Native carnivorous snails, geckos, spiders and a wide range of insects can be found within the swamp ecosystem.
The swamp's inhabitants are vulnerable to introduced animals such as cats, dogs and mustelids. Rats, stoats and ferrets are all capable swimmers, and trapping is regularly carried out to keep their numbers down.
Animal pests such as possums, deer, pigs, rodents and mustelids are controlled by a team of volunteers.