UV-visible irradiation of thiophanate-methyl (TM) led to the formation of nine photoproducts that were characterized by high performance liquid chromatography coupled with high resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). Although carbendazime has been reported in the literature to be the major metabolite and photoproduct of thiophanate-methyl, it was not detected in this study. However, an isomer of carbendazime referred as PP2, which was unambiguously characterized owing to CID experiments, was found in great abundance. Grape berries and cherry tomatoes treated with aqueous solutions of thiophanate-methyl were submitted to irradiation under laboratory conditions. TM and PP2 were detected in both peel and flesh of berries. The ability of TM and PP2 to pass through the fruit skin has been shown to be highly compound and matrix dependent. In vitro bioassays on Vibrio fischeri bacteria showed that the global ecotoxicity of the TM solution increases significantly with the irradiation time. PP2 should likely contribute to this ecotoxicity enhancement since in silico estimations for Daphnia magna provide a LC50 value seven times lower for PP2 than for the parent molecule.