The coastal-aquifer system of Manhasset Neck, Nassau County, New York, has been stressed by pumping, which has led to saltwater intrusion and the abandonment of one public-supply well in 1944. Measurements of chloride concentrations and water levels in 2004 from the deep, confined aquifers indicate active saltwater intrusion in response to public-supply pumping. A numerical model capable of simulating three-dimensional variable-density ground-water flow and solute transport in heterogeneous, anisotropic aquifers was developed using the U.S. Geological Survey finite-element, variable-density, solute-transport simulator SUTRA, to investigate the extent of saltwater intrusion beneath Manhasset Neck. The model is composed of eight layers representing the hydrogeologic system beneath Manhasset Neck. Four modifications to the area?s previously described hydrogeologic framework were made in the model (1) the bedrock-surface altitude at well N12191 was corrected from a previously reported value, (2) part of the extent of the Raritan confining unit was shifted, (3) part of the extent of the North Shore confining unit was shifted, and (4) a clay layer in the upper glacial aquifer was added in the central and southern parts of the Manhasset Neck peninsula. Ground-water flow and the location of the freshwater-saltwater interface were simulated for three conditions (time periods) (1) a steady-state (predevelopment) simulation of no pumping prior to about 1905, (2) a 40-year transient simulation based on 1939 pumpage representing the 1905-1944 period of gradual saltwater intrusion, and (3) a 60-year transient simulation based on 1995 pumpage representing the 1945-2005 period of stabilized withdrawals. The 1939 pumpage rate (12.1 million gallons per day (Mgal/d)) applied to the 1905-1944 transient simulation caused modeled average water-level declines of 2 and 4 feet (ft) in the shallow and deep aquifer systems from predevelopment conditions, respectively, a net decrease of 5.2 Mgal/d in freshwater discharge to offshore areas and a net increase of 6.9 Mgal/d of freshwater entering the model from the eastern, western, and southern lateral boundaries. The 1995 pumpage rate (43.3 Mgal/d) applied to the 1945-2005 transient simulation caused modeled average water-level declines of 5 and 8 ft in the shallow and deep aquifer systems from predevelopment conditions, respectively, a net decrease of 13.2 Mgal/d in freshwater discharge to offshore areas and a net increase of 30.1 Mgal/d of freshwater entering the model from the eastern, western, and southern lateral boundaries. The simulated decrease in freshwater discharge to the offshore areas caused saltwater intrusion in two parts of the deep aquifer system under Manhasset Neck. Saline ground water simulated in a third part of the deep aquifer system under Manhasset Neck was due to the absence of the North Shore confining unit near Sands Point. Simulated chloride concentrations greater than 250 milligrams per liter (mg/L) were used to represent the freshwater-saltwater interface, and the movement of this concentration was evaluated for transient simulations. The decrease in the 1905-1944 simulated freshwater discharge to the offshore areas caused the freshwater-saltwater interface in the deep aquifer system to advance landward more than 1,700 ft from its steady-state position in the vicinity of Baxter Estates Village, Long Island, New York. The decrease in the 1945-2005 simulated freshwater discharge to the offshore areas caused a different area of the freshwater-saltwater interface in the deep aquifer system to advance more than 600 ft from its steady-state position approximately 1 mile south of the Baxter Estates Village. However, the 1945-2005 transient simulation underestimates the concentration and extent of saltwater intrusion determined from water-quality samples collected from wells N12508 and N12793, where measured chloride concentrations increased from 625 and 18 mg/L in 1997 t