Terrestrial enhanced rock weathering (ERW) is reckoned as a robust method to contribute to stabilizing atmospheric carbon and combat global warming. The method is particularly a matter of interest in agricultural soil, offering a vast opportunity for the application of crushed silicate minerals and secondary carbonate accumulation and migration. Although the applicability of this practice is well acknowledged, its impact on the geochemical alteration of soil vertical profile, particularly deeper layers, is less discussed in the literature. Moreover, the effect of irrigation and percolation regimes, as influenced by ambient conditions, is also not well-reported and characterized. In the present study, we utilized a high amendment rate (50 t/ha) of wollastonite skarn, a fast-weathering silicate mineral, to uncover the alterations in topsoil and subsoil as well as effluent water over a through a soil column experiment over five months, under more controlled (indoor) and less controlled (outdoor) ambient and irrigation conditions. The results indicate more conspicuous modification of parameters in shallow layers of soil compared to deeper ones, explicitly in the rain-fed setup. Silicate amendment induced an increase of 6.53 and 2.85 tCO2/ha (in the form of pedogenic carbonate (PC)) over the profile of soil (0–60 cm) under periodic and rain-fed water regimes, respectively. The silicate treatment was also found to be effective toward rising pH and electrical conductivity of topsoil (0–15 and 15–30 cm layers) and leachate, and a measurably greater release of Ca2+ and Mg2+ in the column effluent. We estimate a carbon drawdown ratio (carbonate/bicarbonate) of ≈15:1 in this study, showing that PC formation is a more significant weathering indicator than leachate bicarbonate export in the shorter term for a fast-weathering mineral in pH-neutral soils and moderate irrigation regime. Such observations are valuable for developing carbon drawdown quantification methods suitable for a variety of agricultural lands and global regions.