Manganese (Mn) concentrations in approximately 32,000 groundwater analyses from more than 4800 monitoring wells in northern Germany were evaluated. This region was considered well suited to study Mn in shallow groundwater in unconsolidated sediments. Spearman rank correlation was used to correlate between redox-sensitive parameters and the Mann–Kendall test for an evaluation of temporal trends. Manganese concentrations varied over two orders of magnitude and more than 40% of the wells had concentrations above 0.3 mg/L. Median Mn concentrations in the major hydrogeological units, the Geesten, tidal wetlands, and fluviatile lowlands were 0.12 mg/L, 0.46 mg/L, and 0.27 mg/L, respectively. Separating the data by land use, the median concentrations were 0.20 mg/L for arable land, 0.15 mg/L for forests, and 0.24 for grassland. Calculated background concentrations of Mn varied from <0.25 mg/L to 4.79 mg/L. A new parameter, ∆Mn-Fe, defined as the concentration difference between Mn and Fe in mg/L together with nitrate concentrations exceeding 50 mg/L was used to identify the fertilizer-borne input of nitrate. However, the factor controlling Mn occurrence seemingly was the depth of monitoring wells and the screen-length. Elevated concentrations of Mn and a high ∆Mn-Fe were generally found in shallow wells and wells with short screen-lengths.