Pterins, including biopterin prevalent during cyanobacterial blooms, are nitrogen-containing heterocyclic compounds ubiquitous in both natural and engineered environments. However, their roles and associated human risks in water treatment remain poorly understood. This study systematically investigated the kinetics, disinfection byproducts (DBPs), and toxicity of biopterin in chlorination. For deciphering the reaction kinetics, 1,3,5-trimethoxybenzene proved to be a more effective chlorine quencher than the commonly used reducing agents, as it preserved N-chlorinated intermediates without reversing them back to biopterin. The pH-dependent kinetics demonstrated that both chlorine and biopterin species had a significant influence on the reaction rates, with deprotonated biopterin exhibiting a markedly higher reactivity toward HClO/ClO-. Based on time-of-flight mass spectrometry, ten transformation products (TPs) including seven halogenated N-Cl ones, have been identified for the first time. These cyclic TPs were transformed into various aliphatic carbonaceous and nitrogenous DBPs during the subsequent chlorination process. Notably, theoretical predictions and the luminescent bacteria assay confirmed potential higher toxicities of these products than biopterin. These findings highlight the potential risks of pterins during water disinfection and provide a reference framework for accurately revealing the chlorination behavior of emerging nitrogenous chemicals.