The permutations of geomorphological, pedological and microclimatic environments support diverse vegetation types, for which 58 floristic communities have been recognised within 13 structural forms.

Eucalypt forest and woodland, heath and mangroves occupy most of the area, with isolated patches of rainforest on sheltered steep slopes and swamp communities in the sand dunes in the east of the place.

[1] The eastern shoreline largely consists of long sandy beaches and small rocky headlands, behind which rise the high and generally linear sand dunes of Cape Manifold and Freshwater.

Species of migratory birds that were recorded as abundant on the tidal mudflats of Shoalwater Bay during the summer of 1991–1992 include the lesser golden plover (Pluvialis fulva), bar-tailed godwit (Limosa limosa), whimbrel (Numenius madagascariensis), grey-tailed tattler (Tringa brevipes,) red-necked stint (Calidris ruficollis), terek sandpiper (Xenus cinereus), great knot (Calidris tenuirostris), and the fork-tailed swift (Apus pacificus).

The resultant steep rainfall gradient, from 1,800 millimetres (71 in) in the east to 900, in the west, together with the diverse landforms contributes to the high biodiversity recorded in the place.

A number of feral animals occur within the place including horses, cattle, pigs, rabbits, cane toads, goats and foxes.

[1] The Shoalwater Bay Military Training Area represents the largest coastal wilderness between Nadgee in southern New South Wales and the Cape Melville/Starcke Holding Area on Cape York Peninsula.The place is significant in demonstrating a range of coastal, sub-coastal and aquatic landscapes and ecosystems, which occur in a relatively natural state and which generally, exhibit a high degree of integrity and diversity.

Shoalwater Bay contains landforms of undisturbed depositional sequences resulting from the action of wind (dunes) and water (beach ridges).

These dune systems differ from other coastal and island sand masses in Queensland in that they demonstrate fewer episodes of instability and contain a much lower number of perched lakes.

Unusual plant associations are demonstrated in the gradation from the wet coastal forests in the east of the place to the semi-arid tree species of poplar box (Eucalyptus populnea), bulloak (Allocasuarina luehmanniiand), and Melaleuca spp on the dry ridges occurring above the seasonally waterlogged valleys and swamp communities in the western portion of the place.

[1] The high diversity of landscape types, the steep climatic gradient, and place's location near the junction of the Central Mackay Coast, Brigalow Belt Northern and Brigalow Belt South biogeographic regions accounts for the high numbers of plant, animal and fish species and sub-species that are at, or near, their known southern or northern distribution limits.

Shoalwater Bay thus provides important habitat for many species that are regionally endemic and supports the view that the place is a refugium that has allowed the survival of plants and animals that were far more widespread in the evolutionary past.

CSIRO has established twenty permanent reference sites within the place with research yielding information with important implications for the management of land in eastern Australia.

Four animal species considered vulnerable in Queensland also occur in the place including the glossy black cockatoo (Calyphorhynchus lathami erebus), the beach thicknee (Esacus neglectusand) the northern sheath-tailed bat (Taphozous australis).

This is one of the largest concentrations of this species along the east Australian coast, and Shoalwater Bay is one of the few large shallow waterways in Queensland where turtles are relatively free from the impacts of human activities.

[4][1] Fauna listed as vulnerable in Queensland include; the glossy black cockatoo (Calyptorhynchus lathami), the powerful owl (Ninox strenua), the beach thicknee (Esacus neglectus), and the northern sheath-tail bat (Tapozous australis) .

Research includes: marine processes and benchmark monitoring of marine animals; geomorphological and pedological studies to help understand the natural processes of dune formation; ecological studies into progressive and retrogressive succession of plant communities, fire ecology, the effects of rainfall, topographic and other gradients on the distribution of vegetation, and the interaction of climate, geology, soils and vegetation.

[1] CSIRO has established at least 20 permanent reference sites in the area, and research in the place is yielding information with important implications for the management of land in eastern Australia.

[10][1] This Wikipedia article was originally based on Shoalwater Bay Military Training Area, entry number 105545 in the Australian Heritage Database published by the Commonwealth of Australia 2019 under CC-BY 4.0 licence, accessed on 15 May 2019.