Continuous and excessive use of organophosphorus compounds (OPs) has led to environmental contaminations which raise public concerns. This study investigates the isotope fractionation patterns of OPs in the aquatic environment dependence upon hydrolysis, photolysis and radical oxidation processes. The hydrolysis of parathion (EP) and methyl parathion (MP) resulted in significant carbon fractionation at lower pH (pH 2–7, ε_C = − 6.9 ~ − 6.0‰ for EP, − 10.5 ~ − 9.9‰ for MP) but no detectable carbon fractionation at higher pH (pH 12). Hydrogen fractionation was not observed during any of the hydrolysis experiments. These results indicate that compound specific isotope analysis (CSIA) allows distinction of two different pH-dependent pathways of hydrolysis. Carbon and hydrogen isotope fractionation were determined during UV/H₂O₂ photolysis of EP and tris(2-chloroethyl) phosphate (TCEP). The constant δ²H values determined during the OH radical reaction of EP suggested that the rate-limiting step proceeded through oxidative attack by OH radical on the P<img border="0" alt="double bond; length as m-dash" src="https://cdn.els-cdn.com/sd/entities/dbnd" class="glyphImg">S bond. The significant H isotope enrichment suggested that OH radical oxidation of TCEP was caused by an H-abstraction during the UV/H₂O₂ processes (ε_H = − 56 ± 3‰). Fenton reaction was conducted to validate the H isotope enrichment of TCEP associated with radical oxidation, which yielded ε_H of − 34 ± 5‰. Transformation products of OPs during photodegradation were identified using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS). This study highlights that the carbon and hydrogen fractionation patterns have the potential to elucidate the transformation of OPs in the environment.