We analyze the vertical component of GEONET GNSS measurements in Central Japan and clarify in some of the sites the origin of large annual time variations, as well as the secular variations. Many of these vertical movements may be attributable to the use of groundwater for agriculture, for snow melting, industrial, and hospital usages, etc. and the pumping up of the groundwater mining for refining natural gas and iodine at the production area of natural gas dissolved in water. For this reason, highly accurate monitoring of vertical variations by GNSS observations can provide new observation methods for understanding of not only geodynamics but also hydrology through monitoring groundwater fluctuation, and natural gas and oil resource development through monitoring ground movements caused by mining.