Silicon (Si) is one of the most abundant elements in the earth's crust, although its availability may be affected by some edaphic and abiotic factors such as soil moisture and salinity. In a laboratory experiment, effects of silicon (Si), salinity, and soil moisture on changes of extractable Si, iron (Fe), and manganese (Mn) concentrations were investigated on a sandy loam calcareous soil. The experiment was arranged as a factorial completely randomized design with three replications. Two levels of Si (8 and 200 mg per kg of soil), three salinity levels [0.46 dS m−1, 8 dS m−1 as sodium chloride (NaCl), and 8 dS m−1 as four-salt combination], two soil moisture regimes (–20 kPa and waterlogged), and four incubation times (0, 7, 30, and 45 days) were applied. Salt composition consisted of sodium chloride, sodium sulfate, calcium chloride, and magnesium sulfate at a molar ratio of 4:2:2:1. Acetic acid–extractable Si, Fe, and Mn were determined after 0, 7, 30, and 45 days of incubation. Waterlogging caused significant increase in the extractable Si, Fe, and Mn. Soil salinity of 8 dS m−1, only in the form of sodium chloride, resulted in a marked decrease in extractable Si, Fe, and Mn. Silicon addition enhanced the soil Si concentration, with no effect on Fe and Mn. Equilibrium time for Si and Fe was 30 days, whereas Mn concentration reached to a constant level after 1 week of waterlogging. It was concluded that Si, Fe, and Mn fertilizers should be applied in sufficient amounts to the saline soils to prevent their deficiencies in plants. Meanwhile, overfertilization in waterlogged conditions must be avoided, because of the probability of nutrient imbalance or toxicity.