The Komanoyu hot spring is located at the foot of the active Hokkaido-Komagatake stratovolcano in Japan. The manganese (Mn) wad is precipitated from the Komanoyu hot spring water by biomineralization processes. Four sediment cores of ~12–20 cm long were collected from the hot spring-derived pond to determine physicochemical conditions in the Mn wad sediments by rock magnetic analyses. Based on rock magnetic measurements, the main magnetic mineral throughout the cores is titanomagnetite. The observed low-temperature (LT) properties between ~20 and ~30 K do not correspond with any previously reported magnetic properties of major magnetic minerals or rhodochrosite. Selected Mn ore samples were subjected to LT magnetic analyses, and unique LT characterizations were found for each sample. The results show that the observed LT properties of Mn wad sediments likely indicate the presence of Mn oxides. Further, rock magnetic measurements indicate that the absence of maghemite and/or magnetite with superparamagnetic minerals at just a few centimeters below the top of cores were likely caused by a selective dissolution process, suggesting the reducing condition in the Mn wad sediment column. The results indicate that the changes of the rock magnetic properties are likely caused by this early diagenetic process that would be promoted by microbially induced degradation of organic matter and LT magnetic measurements could be an effective method to identify manganese minerals in sediments.