Understanding transient nitrogen (N) storage and transformation in the deep vadose zone is critical for controlling groundwater contamination by nitrate. The occurrence of organic and inorganic forms of carbon (C) and nitrogen and their importance in the deep vadose zone is not well characterized due to difficulty in sampling and limited studies. We sampled and characterized these pools beneath 27 croplands with different vadose zone thicknesses (6–45 m). We measured nitrate and ammonium in different depths for the 27 sites to evaluate inorganic N storage. We measured total Kjeldahl nitrogen (TKN), hot-water extractable organic carbon (EOC), soil organic carbon (SOC), and δ¹³C for two sites to understand the role of organic N and C pools in N transformations. Inorganic N stocks in the vadose zone were 21.7–1043.6 g m⁻² across 27 sites; the thicker vadose zone significantly stored more inorganic N (p < 0.05). We observed significant reservoirs of TKN and SOC at depths, likely representing paleosols that may provide organic C and N to subsurface microbes. The occurrence of deep C and N needs to be addressed in future research on terrestrial C and N storage potential. The increase of ammonium and EOC and δ¹³C value in the proximity of these horizons is consistent with N mineralization. An increase of nitrate, concurrent with the sandy soil texture and the water-filled pore space (WFPS) of 78 %, suggests that deep vadose zone nitrification may be supported in vadose zones with organic-rich layers such as paleosol. A profile showing the decrease of nitrate concentrations, concurrent with the clay soil texture and the WFPS of 91 %, also suggests denitrification may be an important process. Our study shows that microbial N transformation is possible even in deep vadose zone with co-occurrence of C and N sources and controlled by labile C availability and soil texture.