Groundwater is a vital freshwater resource for both humans and ecosystems. Achieving sustainable management requires a detailed knowledge of the aquifer structure and of its behavior in response to climatic and anthropogenic forcing. Traditional monitoring is carried out using piezometer networks, and recently complemented with new geophysical or satellite-based observations. These techniques survey either local (small-scale) water systems or regional areas (large scale) but, to date, adequate observation tools are lacking at the water management scale (i.e. several tens of kms), which is generally explored by modeling. Using 30 years of continuous recording by four seismic stations of the Gräfenberg Array (Germany), we demonstrate that long-term observations of velocity variations (approximately 0.01%) of surface waves can be extracted from such recordings of ocean-generated seismic noise. These small variations can be explained by changes to mechanical properties of the complex aquifer system in the top few hundred meters of the crust. The velocity changes can be interpreted as effects of temperature diffusion and water storage changes. Seismic noise recordings may become a new and valuable tool to monitor heterogeneous groundwater systems at mesoscale, in addition to existing observation methods.