Soil chamber measurements of <em>δ</em>(O<sub>2</sub>/N<sub>2</sub>), CO<sub>2</sub> amount fractions, and the <em>δ</em>(<sup>18</sup>O) of O<sub>2</sub> in air (<em>δ</em><sub>atm</sub>(<sup>18</sup>O)) were conducted at a forest site in Takayama (TKY), Japan, and at agricultural fields in Tsukuba (TKB) and Miyakojima (MYK), Japan. The latter fields included plots with and without crushed rock application for the evaluation of enhanced rock weathering (ERW) for carbon dioxide removal (CDR). The 7-year average O<sub>2</sub>:CO<sub>2</sub> exchange ratios for soil–air O<sub>2</sub> and CO<sub>2</sub> fluxes were 1.10±0.01 at TKY, whereas the two-year averages at the agricultural fields varied from 0.38 to 4.32. Assuming soil respiration yields an O<sub>2</sub>:CO<sub>2</sub> ratio of 1.1, we partitioned CO<sub>2</sub> fluxes into soil respiration and abiotic reactions including CO<sub>2</sub> dissolution and dissociation. At TKB, the low CO<sub>2</sub> emissions from the basalt-applied plot were attributed to reduced soil respiration. In contrast, at MYK, both plots showed abiotic CO<sub>2</sub> uptake, comparable to modeled CDR rates for ERW, regardless of basalt/olivine application. These results suggest that inherent soil processes such as alkalinity-driven CO<sub>2</sub> absorption and leaching, rather than rock application, were responsible for the observed net CDR, questioning the impact of ERW at these sites. Our analytical approach effectively quantified CDR by accounting for both biotic and abiotic processes. The isotopic effect of soil respiration (<em>ε</em><sub>SR</sub>) from <em>δ</em>(O<sub>2</sub>/N<sub>2</sub>) and <em>δ</em><sub>atm</sub>(<sup>18</sup>O) was substantially lower at TKB and MYK than previously reported. Revising the plausible global average eSR to 14.6 ‰ would reduce the modeled Dole–Morita effect from 23.16 ‰ to 22.71 ‰.