Iron and manganese differentiation were analyzed in the lakes, rivers, springs, and groundwaters the Suwałki Landscape Park (SLP) in July 2009. The major aim of this study was to evaluate the relationship between manganese and iron concentrations and other physical and chemical water parameters. The waters of SLP differed in terms of fractional composition of manganese and iron. Higher concentrations of total iron and manganese were observed in groundwaters (1645 μgFe/dm³, 949 μgMn/dm³). The fractional composition of iron and manganese depends on the amount of dissolved organic carbon (DOC) related to the development of metaloorganic complexes. Manganese compounds are more volatile in an aquatic environment than iron compounds, as manifested in the variable fractional composition of manganese in the lakes of SLP.