Abstract The effects of injecting oxic water from the New York city (NYC) drinking-water supply and distribution system into a nearby anoxic coastal plain aquifer for later recovery during periods of water shortage (aquifer storage and recovery, or ASR) were simulated by a 3-dimensional, reactive-solute transport model. The Cretaceous aquifer system in the NYC area of New York and New Jersey, USA contains pyrite, goethite, locally occurring siderite, lignite, and locally varying amounts of dissolved Fe and salinity. Sediment from cores drilled on Staten Island and western Long Island had high extractable concentrations of Fe, Mn, and acid volatile sulfides (AVS) plus chromium-reducible sulfides (CRS) and low concentrations of As, Pb, Cd, Cr, Cu and U. Similarly, water samples from the Lloyd aquifer (Cretaceous) in western Long Island generally contained high concentrations of Fe and Mn and low concentrations of other trace elements such as As, Pb, Cd, Cr, Cu and U, all of which were below US Environmental Protection Agency (USEPA) and NY maximum contaminant levels (MCLs). In such aquifer settings, ASR operations can be complicated by the oxidative dissolution of pyrite, low pH, and high concentrations of dissolved Fe in extracted water. The simulated injection of buffered, oxic city water into a hypothetical ASR well increased the hydraulic head at the well, displaced the ambient groundwater, and formed a spheroid of injected water with lower concentrations of Fe, Mn and major ions in water surrounding the ASR well, than in ambient water. Both the dissolved O 2 concentrations and the pH of water near the well generally increased in magnitude during the simulated 5-a injection phase. The resultant oxidation of Fe 2+ and attendant precipitation of goethite during injection provided a substrate for sorption of dissolved Fe during the 8-a extraction phase. The baseline scenario with a low (0.001 M) concentration of pyrite in aquifer sediments, indicated that nearly 190% more water with acceptably low concentrations of dissolved Fe could be extracted than was injected. Scenarios with larger amounts of pyrite in aquifer sediments generally resulted in less goethite precipitation, increased acidity, and increased concentrations of dissolved Fe in extracted water. In these pyritic scenarios, the lower amounts of goethite precipitated and the lower pH during the extraction phase resulted in decreased sorption of Fe 2+ and a decreased amount of extractable water with acceptably low concentrations of dissolved Fe (5.4 × 10 −6 M). A linear decrease in recovery efficiency with respect to dissolved Fe concentrations is caused by pyrite dissolution and the associated depletion of dissolved O 2 (DO) and increase in acidity. Simulations with more than 0.0037 M of pyrite, which is the maximum amount dissolved in the baseline scenario, had just over a 50% recovery efficiency. The precipitation of ferric hydroxide minerals (goethite) at the well screen, and a possible associated decrease in specific capacity of the ASR well, was not apparent during the extraction phase of ASR simulations, but the model does not incorporate the microbial effects and biofouling associated with ferric hydroxide precipitation. The host groundwater chemistry in calcite-poor Cretaceous aquifers of the NYC area consists of low alkalinity and moderate to low pH. The dissolution of goethite in scenarios with unbuffered injectate indicates that corrosion of the well could occur if the injectate is not buffered. Simulations with buffered injectate resulted in greater precipitation of goethite, and lower concentrations of dissolved Fe, in the extracted water. Dissolved Fe concentrations in extracted water were highest in simulations of aquifers (1) in which pyrite and siderite in the aquifer were in equilibrium, and (2) in coastal areas affected by saltwater intrusion, where high dissolved-cation concentrations provide a greater exchange of Fe 2+ (FeX 2 ). Results indicate that ASR in pyrite-bearing, Cretaceous aquifers of the NYC area can be a cost effective way to both store drinking water supplies and significantly reduce ambient concentrations of dissolved Fe.