This study investigates the efficacy of the system O3/sunlight radiation compared to dark ozonation when treating pharmaceuticals compounds of different reactivity, namely bezafibrate, cotinine, and iopamidol. Results show the beneficial effects of simulated sunlight radiation (300–800 nm) when treating ozone recalcitrant compounds such as cotinine and iopamidol. The system O3/sunlight radiation increased mineralization extent in all cases if compared to dark ozonation. Transformation products identified in individual runs suggest that amine oxidation and further alkyl chain attack is the main route of bezafibrate ozonation. Hydroxylation seems to be the preferential path in cotinine abatement while H abstraction from alcoholic moieties is suggested in the case of iopamidol. Toxicity of intermediates was approximately evaluated by QSAR methodologies and experimentally through Daphnia Magna survival after 24 h. As a rule of thumb, initial intermediates generated are even more toxic than parent compounds, however, after 120 min of treatment, toxicity significantly decreased. Amongst the most toxic compounds generated: 4-Chlorobenzoyltyramine, and 4-Chloro-N-[2-(3,4-dihydroxy-phenyl)-ethyl]-benzamide (from bezafibrate), and N-(2-Hydroxy-1-hydroxymethyl-ethyl)-N'-(1-hydroxymethyl-2-oxo-ethyl)-5-(2-hydroxy-propionylamino)-2,4,6-triiodo-isophthalamide, N,N′-Bis-(1-hydroxymethyl-2-oxo-ethyl)-5-(2-hydroxy-propionylamino)-2,4,6-triiodo-isophthalamide, and N-(1-Hydroxymethyl-2-oxo-ethyl)-5-(2-hydroxy-propionylamino)-2,4,6-triiodo-isophthalamide (from iopamidol) were identified.