Longneck Lagoon is within the Cumberland Plain Woodland (CPW), which is a critically endangered ecological community that stretches across the Sydney basin.

Ecological communities are only listed as critically endangered if there is a high risk that they will become extinct in the immediate future. In 1998, the CPW was estimated to cover only 8.8% of the original land that it covered prior to European settlement. Between 1997 and 2007, a further 5.2% of the CPW was lost due to land clearing for farming, urban expansion, etc. The remaining woodlands are fragmented, meaning they exist in multiple small pockets among urban development.

The woodland around Longneck Lagoon is part of Scheyville National Park and is therefore managed by NSW National Parks and Wildlife Services.

Transitional Melaleuca Forest

The western margin of the catchment is dominated by paperbark forest. The main species of paperbark found here are Melaleuca styphelioides, Melaleuca linariifolia and Melaleuca decora. When the Melaleucas are in flower they attract a variety of bird life. 

Freshwater Reed Swamp

A variety of reeds and rushes such as Cumbungi (Typha orientalis) and Common Reed (Phragmites) which are adapted to permanent water inundation are growing in the lagoon. A tall forest consisting of paperparks and swamp she-oaks (Casuarina glauca) also surrounds large sections of the lagoon. 

This sedgeland and rushland ecosystem supports a variety of native animals including the Longnecked Tortoise (Chelodina longicollis), Eastern Water Dragons (Intellagama lesueurii lesueurii), bats, frogs, native fish and eels. Like many of the wetland environments within the Hawkesbury-Nepean Catchment, the lagoon also supports an abundant bird population. Common species of birds found in the lagoon include the Dusky Moorhen (Gallinula tenebrosa), Swamp Hen (Porphyrio porphyrio), Great Egret (Ardea alba) and Black Swan (Cygnus atratus). 

Introduced species

A number of animals have been introduced to the Longneck Lagoon Catchment since European settlement including rabbits, cats, foxes, deer and fish. Of these introduced species, the European Carp (Cyprinus carpio), has been one of the most detrimental to the lagoon environment. 

While carp are valued in some parts of the world, in North America, Canada and Australia, they are considered invasive pests. Carp are omnivorous feeders, sucking and straining mud from the bottom and sucking insects and plants from the surface. They can negatively impact their surroundings by stirring up sediment, reducing light penetration and smothering plants and fish eggs. High carp densities lead to problems like deteriorating water quality, inhibited visual feeding by other fish and clogging of gills in different species. Their feeding habits also result in the direct removal of aquatic plants, affecting invertebrate populations and destabilising bottom sediments. The consequences of carp in Longneck Lagoon include diminished water quality and decreased abundance and diversity of native species. 

Introduced plants are also a problem in the catchment. Weeds compete with native plant species for nutrients, water, sunlight and space, and can also smother native species. As a result, the animals that rely on native species for food and shelter become threatened. Common weeds found in the catchment include Fireweed (Senecio madagascariensis) and Privet (Ligustrum lucidum and Ligustrum sinense).