Ultrasound-based water treatment is often applied for degradation of stable organic pollutants, such as polycyclic aromatic hydrocarbons and halogenated compounds. Monitoring the degradation process, during the application of ultrasound radiation, is of considerable economical interest. In this work, the possibility of performing on-line spectral analysis during sonication was examined and it was found that direct absorption or fluorescence readings are misleading. Optical monitoring is strongly affected by the absorption and scattering of light by cavitation micro-bubbles and ultrasound induced particulates. A model was developed to account for these effects and to allow for on-line fluorescence analysis. The model takes into account the absorption and scattering coefficients of the micro-bubbles and particulates, as well as their time dependent concentration. The model parameters are found from independent measurements where the pollutants are added to already sonicated pure water. Then, the model is tested for predicting the actual fluorescence behavior during the sonication process. It has been shown that the model allows for recovery of the true degradation data, as obtained by off-line HPLC measurements.