Subtidal shallows support communities of submerged plants similar to those described for Stockport Flats, and freshwater intertidal mudflat and shore communities are also present. Tivoli South Bay is dominated by Eurasian water chestnut, a floating, exotic species. Both the tidal swamp between the bays and the smaller swamp at the mouth of Stony Creek are mixed deciduous communities with well-developed shrub layer and abundant moss species. The clay bluffs and rocky islands support mixed forests dominated by oak, hickory, eastern hemlock, and pine. A large snapping turtle population exists in and around Tivoli North Bay.
Waterfowl use the site extensively during migration and winter.
Many other birds use the site for feeding, breeding, and migratory stop overs. Zebra mussels, an invading exotic species, dominates subtidal rocky areas. Rare plants that occur or that have occurred here include heart leaf plantain, estuary beggar ticks, golden club, ovate spikerush, Parker's pipewort, Nuttall's micranthemum, Eaton's burmarigold, false pimpernel, winged monkey flower, and swamp lousewort. Brick manufacturing was an important early 19th century industry. By the end of the 19th century extensive portions of the shoreland had been converted to large estates, many of them still standing today.