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Photosystem II (PS II) pesticides, recognized as a threat to ecological health, were targeted for reduction in sugarcane farming in Great Barrier Reef (GBR) catchments. Alternative herbicides, the non-PS II herbicides (including glyphosate, paraquat, 2,4-D, imazapic, isoxaflutole, metolachlor, and S-metolachlor), continue to be used in these catchments. However, the potential ecological fate, transport, and off-site environmental effects of non-PS II herbicides, with respect to their usage scheme, local rainfall patterns, and infiltration dynamics, have not been investigated previously. A vadose zone monitoring system, instrumented beneath sugarcane land in a GBR catchment, was applied for real-time tracing of pesticide migration across the unsaturated zone, past the root zone during 2017–2019. The regularly applied pesticides (fluroxypyr and isoxaflutole) exhibited substantial migration through the unsaturated zone. Within 1 month of application of fluroxypyr, it leached to 2.87 m depth in the vadose zone, with declining concentrations with depth. Isoxaflutole, which was applied yearly, was found only once, in November 2018, at 3.28 m depth in the soil profile. Other pesticides (imazapic, metolachlor, glyphosate, and haloxyfop) applied during the same period were not detected in the vadose zone. However, imidacloprid, which was not applied at the site during the monitored period, was detected across the entire vadose zone, revealing substantial resistance to degradation. The results show no evidence of any regularly applied pesticides in the site bores at the end of the study, indicating their ultimate degradation within the vadose zone before reaching the groundwater. [ABSTRACT FROM AUTHOR]