Tivoli Bays is dominated by two large river coves partially surrounded by wooded clay bluffs. The north bay is predominantly intertidal marsh (386 acres/156 hectares) with a well-developed network of tidal creeks and pools. A similar network of creeks and pools is beginning to form in the south bay's shallows and mudflats (288 acres/115 hectares). The main tributaries are the Stony Creek and the Saw Kill, which drain a combined watershed of about 48 square miles (124 sq. km).
The tidal marshes at Tivoli North Bay are dominated by narrowleaf cattail (Typha angustifolia), spatterdock (Nuphar advena) and wild rice (Zizania aquatica) interspersed with purple loosestrife (Lythrum salicaria) and common reed (Phragmites australis). Subtidal shallows support communities of submerged plants including water celery (Vallisneria americana). Tivoli South Bay is dominated by Eurasian water chestnut (Trapa natans), a floating, non-native species. Tidal swamps are mixed deciduous communities with a well-developed shrub layer and abundant moss species.
Tivoli Bays was designated as a New York State Important Bird Area in 1997. This designation was awarded on the basis of the documented occurrence of breeding least bitterns (Ixobrychus exilis), Virginia rail (Rallus limicola), sora (Porzana carolina), common moorhen (Gallinula chloropus), and marsh wren (Cistothorus palustris). Tivoli Bays is also designated as a New York Bird Conservation Area in recognition of its unique breeding marsh bird community, its prominence as a staging area for migrating waterfowl including large numbers of black ducks (Anas rubripes), and its upland forest and shrub areas which provide important migratory stopover habitat for warblers, flycatchers, sparrows, blackbirds, and many other songbird migrants. A 2005 marsh bird survey observed numerous resident marsh bird species including Virginia rail, red-winged blackbird (Agelaius phoeniceus), marsh wren, least bittern, American bittern (Botaurus lentiginosus), and swamp sparrow (Melospiza georgiana). Raptor species commonly observed at Tivoli Bays include bald eagle (Haliaeetus leucocephalus), osprey (Pandion haliaetus), and northern harrier (Circus cyaneus). Other common wildlife observed include snapping turtle (Chelydra serpentina), muskrat (Ondatra zibethicus) and beaver (Castor canadensis).
