Singlet oxygen (1O2) is a highly reactive species formed through solar irradiation of organic matter in environmental waters. Implicated in a range of reactions, it has proven difficult to quantify its spatial distribution in natural waters. We assessed the microheterogeneous distribution of 1O2 in irradiated solutions containing chromophoric dissolved organic matter (CDOM) by using molecular probes of varying hydrophobicity. The apparent 1O2 concentrations ([1O2]app), measured by recently developed hydrophobic trap-and-trigger chemiluminescent probe molecules, were orders of magnitude higher than those measured by the conventional hydrophilic probe molecule furfuryl alcohol. The differential [1O2]app values measured by these probes reflect a steep concentration gradient between the CDOM macromolecules and the aqueous phase. A detailed kinetic model based on the data predicts probabilistic 1O2 distributions under different solvent conditions.