Nitrate is a pervasive aquatic contaminant of global environmental concern. In nature, the most effective nitrate reduction reaction (NRR) is catalyzed by nitrate reductase enzymes at neutral pH, using a highly‐conserved Mo center ligated mainly by oxo and thiolate groups. Mo‐based NRR catalysts mostly function in organic solvents with a low water stability. Recently, an oxo‐containing molybdenum sulfide nanoparticle that serves as an NRR catalyst at neutral pH was first reported. Herein, in a nanoparticle‐catalyzed NRR system a pentavalent MoV(=O)S4 species, an enzyme mimetic, served as an active intermediate for the NRR. Potentiometric titration analysis revealed that a redox synergy among MoV−S, S radicals, and MoV(=O)S4 likely play a key role in stabilizing MoV(=O)S4, showing the importance of secondary interactions in facilitating NRR. The first identification and characterization of an oxo‐ and thiolate‐ligated Mo intermediates pave the way to the molecular design of efficient enzyme mimetic NRR catalysts in aqueous solution.