Manganese (Mn) is one of the most abundant metals naturally present in the environment, but currently, it also represents an important factor of environmental contamination due to intense human activity. To investigate the nature of the presence of concentrations above the limits (CSC) established by Legislative Decree 152/06 for manganese in the groundwater underlying a non-hazardous solid waste plant, a study was carried out on the geochemical characteristics of the aquifers present in the study area. The study aimed to determine the natural background value (NBV) of Mn in the groundwater underlying the study area, according to the “Guidelines for Determining the Background Values of Soils and Groundwater” of ISPRA. Indeed, NBV assessment and site-specific considerations can help identify any specific sources of contamination in an area. In the study area, the chemical–physical and geochemical parameters of the water of 11 piezometers were analyzed. Subsequently, statistical tests were applied to detect an NBV identified as 192.3 µg/L, therefore much higher than the CSC, due to possible ongoing local phenomena linked to the geogenic conditions of the soil, which could determine high manganese values. In fact, in the study area, some lithologies favor establishing anaerobic environments and releasing manganese in the groundwater as hydroxides. Consequently, this process can lead to high manganese concentrations, even exceeding legal limits.