This dataset and model archive provides geochemical modeling input and selected output data used in simulations of seawater restoration on historically diked salt marshes. Biogeochemical changes resulting from seawater reintroduction were simulated using the computer program PHREEQC (Parkhurst and Appelo, 2013) to help support efforts to restore tidal flow and associated estuarine habitat to diked marshes, including the Herring River estuary in Wellfleet, Massachusetts, on Cape Cod. First, one-dimensional reactive transport models were developed and calibrated using data from Portnoy and Giblin (1997) microcosm experiments of sediment cores to better understand the associated timing and sequence of biogeochemical reactions and their implications to aquatic health. These cores included diked, flooded marsh sediments and subaerially exposed, diked, drained sediments representative of the Herring River diked marsh. Solute concentrations measured in the microcosm experiment data were used to estimate sedimentary organic matter decay rates by matching the timing and magnitude of simulated dissolved ferrous iron and sulfide concentrations. Then, "basecase" models were used to simulate a single flow velocity to better understand biogeochemical conditions over longer time periods and with varying ferric iron source minerals.