This study investigated the release of heavy metals from polluted soil under the pore water flow containing nanobubbles (NBs) to simulate natural ebullition. Three types of NBs (CH4, H2, and CO2) were generated in water and characterized, including bubble size, zeta potential, liquid density, and tension. The flow rate used in column tests was optimized to achieve proper soil fluidization and metal desorption or release. The leachate chemistries were monitored to assess the effect of NBs on conductivity, pH, oxidation–reduction potential (ORP), and dissolved oxygen (DO). The results showed that NBs in the pore water flow were significantly more effective in releasing Pb compared to DI water, with CO2NB water being the most effective and H2NB water being the least effective. CO2NB water was also used to rinse column soil contaminated with four different metals (Pb, Cu, Zn, and Cr), which exhibited different leaching kinetics. Moreover, a convective–dispersion–deposition equation (CDDE) model accurately simulated the leaching kinetics and explained the effects of NBs on the key parameters, such as the deposition rate coefficient (Kd), that affect the released metal transport. The findings could provide new insights into soil pollutant release under ebullition and soil remediation using water wash containing NBs.