The focus is on ‘non-detrital’ Nb in boreal stream waters (dissolved fraction and acid-available particulate fraction) and brackish-water/lacustrine sediments (aqua regia extractable fraction). Spatial patterns, temporal trends and speciation experiments all point to dissolved humic substances and colloidal Fe as the main control of Nb concentrations in stream waters. In addition, clay-silt deposits and/or ore deposits may be responsible for producing local streamwater Nb anomalies. In groundwater in overburden (glacial till) overlying Proterozoic granitoids, dissolved Nb concentrations were about an order of magnitude higher than in stream waters and strongly correlated with dissolved Fe. In the brackish-water sediments, the Nb concentrations (1.33–4.20 ppm) were higher than in the lacustrine ones (0.25–0.53 ppm). To explain this, we assessed the potential role of organic material, biological processes, sulphide mineralogy, silicate mineralogy and input factors. However, none of them could satisfactorily explain the observed Nb geochemical features. Although Nb can be considered relatively immobile, the data presented in this paper show that under certain conditions its abundance in the aquatic environment increases.