The transport and potential toxicity of pesticides in Queensland (QLD) catchments from agricultural areas is a key concern for the Great Barrier Reef (GBR). In 2009, a pesticide monitoring program was established as part of the Australian and QLD Governments’ Reef Plan (2009). Samples were collected at eight End of System sites (above the tidal zone) and three sub-catchment sites. At least two pesticides were detected at every site including insecticides, fungicides, herbicides, and the Reef Plan’s (2009) five priority photosystem II (PSII) herbicides (diuron, atrazine, hexazinone, tebuthiuron and ametryn). Diuron, atrazine and metolachlor exceeded Australian and New Zealand water quality guideline trigger values (TVs) at eight sites. Accounting for PSII herbicide mixtures increased the estimated toxicity and led to larger exceedances of the TVs at more sites. This study demonstrates the widespread contamination of pesticides, particularly PSII herbicides, across the GBR catchment area which discharges to the GBR.