Limestone possesses high performance as a chemical reagent for neutralizing acidic hot spring water. However, the emission of carbon dioxide and formation of large amounts of precipitates such as Ca(OH)2 are big issues during this process. To address this issue, we investigated the utility of crushed gravels of mafic and tuffaceous rocks as a neutralization reagent and the behaviors of rare metals, As and Pb with addition of those rocks. After addition of 5 % mass of rock powders to the acidic hot spring water collected from the Tamagawa Hot Spring, it was observed the increase in the pH of supernatant in all samples. Furthermore, the concentration of all 15 rare earth elements in the solution increased higher than ten-fold of the original concentration of light rare earth elements such as La, Ce and Pr and higher than 5-fold of heavy rare earth elements were recognized in the case of pillow lava, and then it is possible to precipitate rare earth elements by increasing of pH levels. Additionally, toxic elements such as As and Pb as well as Cs in the hot spring water were reduced by 44%, 90% and 96%, respectively. Findings indicate that the dissolution of mafic rocks in acidic hot spring water causes an increased concentration of rare earth elements in the solution, and then to obtain these elements as precipitates due to increase of pH. It is also possible to separate useful rare earth elements and toxic elements by control of pH levels.