Dissolved organic matter (DOM) strongly affects water quality within boreal forest ecosystems. However, how the quality of DOM itself changes spatially is not well understood. In this study, to examine how the diversity of DOM molecules varies in water moving through a boreal forest, the number of DOM molecules in different water samples, i.e., rainwater, throughfall, soil water, groundwater, and stream water was determined using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) in Norway spruce and Scots pine stands in eastern Finland during May and June 2010. The number of molecular compounds identified by FT-ICR MS (molecular diversity) ranged from 865 to 2,194, revealing large DOM molecular diversity in the water samples. Additionally, some of the molecular compounds were shared between different water samples. The DOM molecular diversity linearly correlated with the number of low-biodegradable molecules, such as, lignin-like molecules (lignins), but not with dissolved organic carbon concentration. The number of lignins shared between different sampling locations was larger than that of any other biomolecular class. Our results suggest that low-biodegradable molecules, especially lignins, regulate spatial variations in DOM molecular diversity in boreal forests.