Odorous compounds such as geosmin and 2-methylisoborneol (2-MIB), and nitrogen ions such as ammonium (NH₄+), nitrite (NO₂−), and nitrate (NO₃−) are challenging chemicals for drinking water treatment. This study aimed at identifying the potential of submerged nanofiltration (NF) membrane treatment for removing these chemicals. In this work, tight NF membranes (p-ESNA and NF90) achieved high removal of odorous compounds (89–98 %) under varying feed temperatures (13–30 °C) and additional salt concentrations (NaCl = 10–20 mM), while a loose NF membrane (NF270) exhibited lower rejection (61–86 %). Conversely, the rejection of nitrogen ions by the two tight NF membranes was low in the submerged configuration (7–39 %), and their rejection significantly decreased with increasing feed salinity (−5–29 %). The loose NF membrane (NF270) even exhibited negative rejections (−4–6 %), likely due to a membrane charge imbalance induced by the Donnan effect, which was exacerbated by competitive divalent sulfate anions. The unsaturated electromigration of NO2− and NO3− anions, driven by the electric field of diffusion potential, can lead to negative rejection at low transmembrane flux. This study identified the capacity and limitations of submerged NF treatment for removing the problematic odorous and nitrogen chemicals.