Pesticide run-off from agricultural land has been identified as a major factor contributing to the declining water quality in adjacent catchments that discharge to the Great Barrier Reef (GBR). Acute and chronic exposure to individual pesticides as well as mixtures, can cause a range of sub-lethal and lethal effects to aquatic organisms. The Australian and Queensland governments have developed end-of-catchment pesticide targets that aim to protect 99% of aquatic species from the adverse effects of pesticide mixtures. However, estimates of “safe” concentrations of pesticides (i.e., water quality guidelines) are required to determine if the detected environmental concentrations could cause harmful effects. Despite over 70 pesticides and their degradation products being detected in GBR catchment waterways and in the GBR lagoon, only a small number of these pesticides have water quality guidelines in the Australian and New Zealand Guidelines for Fresh and Marine Water Quality. Here, we discuss the derivation of proposed default guideline values (DGVs) for five pesticides (4-hydroxychlorothalonil, methoxyfenozide, carbendazim, dimethoate and 2,4-D) that are regularly detected in GBR waterways. The proposed DGVs have been derived using the Australian and New Zealand nationally endorsed methods of water quality guidelines for aquatic ecosystem protection. The DGVs will be used to assess the potential risks of these pesticides across GBR catchments, based on monitoring data from the Great Barrier Reef Catchment Loads Monitoring Program. The proposed DGVs can also be incorporated into tools such as the Pesticide Risk Metric and Pesticide Decision Support Tool.