Soil CO2 flux (FCO2) was intensively measured in a natural CO2 emission site located in a tectonically quiescent area, with topographic and geophysical investigation, to estimate annual emissions and causes of focused leaks. FCO2 varied between 6.5 and 2155.4 g/m2/d (median 76.1 g/m2/d; n = 67) within a 612 m2 area situated close to a CO2-rich groundwater well. The threshold value for geogenic FCO2 was determined to be 23 g/m2/d using a Q-Q plot. A FCO2 hotspot was delineated where FCO2 exceeded the threshold. Based on linear regression using air pressure and temperature, the annual CO2 emissions from the hotspot in 2019 were approximately 19 tons/y. According to the 2D electrical resistivity distribution, the subsurface around the well was highly weathered, showing low electrical resistivity (<2000 Ω-m) down to a depth of 50 m, whereas the top layer around the hotspot showed a relatively high electrical resistivity (> 500 Ω-m), implying a resistant unsaturated zone. High signal attenuation and discontinuous and dipping reflectors of ground-penetrating radar signals suggested gaseous CO2 transport through preferential pathways in the resistant near-surface. Based on these and previous hydrochemical results, the extremely high FCO2 in the narrow extent can be explained by a leakage scenario in which the frequent usage of CO2-rich water through the well enhances CO2 degassing, while defects in the well casing accelerate the upward movement of CO2 gas, which flows out through a preferential pathway in the resistant unsaturated zone. This study provides insights into focused leakages through faulty wells and near-surface preferential pathways. In addition, the quantification of annual CO2 emissions through point sources is applicable for assessing natural gas emissions produced by hotspots. The non-negligible emission rate in the hotspot (about 92 g/m2/d) emphasizes the need to quantify natural CO2 emissions in tectonically quiescent areas for risk assessments and carbon budgets.