Freshwater storage in deep aquifers of Brooklyn and Queens, New York, USA, is under consideration as an emergency water supply for New York City. The purpose of a New York City storage and recovery system is to provide an emergency water supply during times of drought or other contingencies and would entail longer-term storage phases than a typical annual cycle. There is concern amongst neighboring coastal communities that such a system would adversely impact their local water supplies via increased saltwater intrusion. This analysis uses three-dimensional modeling of variable-density ground-water flow and salt transport to study conditions under which hypothetical aquifer storage and recovery (ASR) may not adversely impact the coastal water supplies. A range of storage, pause, and recovery phase lengths and ASR cycle repetitions were used to test scenarios that emphasize control of potential saltwater intrusion. The USGS SUTRA code was used to simulate movement of the freshwater-saltwater transition zones in a detailed model of the upper glacial, Jameco, Magothy, and Lloyd aquifers of western Long Island, New York. Simulated transition zones in the upper glacial, Jameco, and Magothy aquifers reach a steady state for 1999 stress and recharge conditions within 1 ka; however, saltwater encroachment is ongoing in the Lloyd (deepest) aquifer, for which the effects of the rise in sea level since deglaciation on transition zone equilibration are retarded by many ka due to the thick, overlying Raritan confining unit. Pumping in the 20th century has also caused widening and landward movement of the Lloyd aquifer transition zone. Simulation of scenarios of freshwater storage by injection followed by phases of pause and recovery by extraction indicates that the effect of net storage when less water is recovered than injected is to set up a hydraulic saltwater intrusion barrier in the Lloyd aquifer which may have beneficial effects to coastal water users.