In small-scale water systems, the measurement of quality of raw water in running water is generally implemented when the quality of water is stable and frequency of measurement is low. However, units such as water temperature and pH, which are easily monitored, are frequently measured. In establishing an improvement plan for a water treatment system, the range of concentration of the target material present in the raw water of the running water provides relevant information. If the concentration of target material can be specified by the quality of water of data items that are measured daily, inverse estimation of the range of concentration is possible as well. In this paper, we took note of manganese in the raw water from Ogasawara-mura, Tokyo, and estimated the manganese concentration in the raw water of the running water for the past five years. Based on the results obtained, we have proposed a manganese removal system, considering the current situation and geographical conditions of Ogasawara-mura.