© 2016 IOP Publishing Ltd. Moisture content measurements of rice kernels and soil are important for agriculture. Therefore, in this study, a new measurement method using the diamagnetic characteristics of water was developed for measurements of the moisture content of rice kernels and soil. The magnetic characteristics of the samples were determined using a magnetometer developed by us based on a superconducting quantum interference device. Because of the diamagnetic characteristics of water, the susceptibility of rice kernels became more negative with increasing moisture content. In the case of soil, which is a mixture of diamagnetic and ferromagnetic materials, a second-harmonic detection method using AC with DC bias magnetic field was applied to reduce the influence of the ferromagnetic signal. The intensity of the second-harmonic signal of a soil was determined to be proportional to its moisture content.