Accurate assessment of organic pollution plays a vital role in environmental protection, administration, and legislation. Methodology involving the evaluation of dichromate-based chemical oxygen demand (CODCr) has been widely used for assessing organic pollution in water due to convenience, simplicity, and repeatability. Some nitrogenous organic compounds exhibit very low CODCr / theoretical oxygen demand (ThOD) ratios, which are termed inoxidizable nitrogenous organic compounds (INOCs) in this study. However, not much attention has been paid to their ubiquitous presence and intrinsic properties. Here, we aimed to determine the under-reporting potential of INOCs when assessing organic water pollution via CODCr and reveal the mechanisms underlying such under-reporting. CODCr reported only 0%–20% of the theoretical values of short-chain organic amines and pyridine derivatives, thereby posing severe challenges to both the treatment and reclamation of wastewater. Density functional theory calculations revealed that the use of dichromate-based transformation of INOCs to highly stable protonated/ionic forms under acidic conditions may lead to incomplete reactions, resulting in a significant under-reporting potential of INOCs. Our results may serve as a basis for governments, industries, and other stakeholders to respond more effectively to challenges posed by INOCs.