The assessment of oxidative pollutant biotransformation by compound specific isotope analysis (CSIA) is often complicated by the variability of kinetic isotope effects associated with carbon oxygenation in enzymatic reactions. Here, we illustrate how information about the kinetics of oxidative biocatalysis by flavin-dependent monooxygenases (FMOs) enables one to assess if CSIA could be applied for tracking contaminant biodegradation. In "cautious" FMOs, which form reactive flavin (hydro)peroxide species after substrate binding, the monooxygenation of organic compounds is not rate-determining and consequently does not lead to substrate isotope fractionation. Conversely, "bold" FMOs generate hydroperoxides regardless of substrate availability, and substrate disappearance is thus subject to isotope fractionation trends, which are typical for hydroxylation reactions. Because monooxygenations of aromatic moieties are often initial steps of organic pollutant transformation, knowledge of the kinetics of FMOs and other oxidative enzymes can support decisions regarding the use of CSIA.