Pesticide active ingredients (PAIs) are regularly detected in the rivers, creeks, wetlands, and inshore waterways that discharge to the Great Barrier Reef (GBR) lagoon. Pesticide active ingredients detected above ecologically protective concentrations may pose a hazard and risk to aquatic species. The ability to assess this hazard and risk is reliant on the availability of water quality guidelines, which are only available for a limited number of PAIs detected in GBR catchment waterways. Unendorsed guideline values, known as ecotoxicity threshold values (ETVs) were developed in part one of this study for active ingredients in two fungicides (4-hydroxychlorothalonil (fungicide degradate) and carbendazim) and two insecticides (dimethoate and methoxyfenozide) that are commonly detected in GBR catchment waterways. In the current study, the hazard and risk posed by these PAIs was assessed by comparing the ETVs to environmental monitoring data from the Great Barrier Reef Catchment Loads Monitoring Program. Exceedances of the concentrations that should protect 99 % of aquatic species (i.e., PC99) were observed for all four pesticides. Detected concentrations of 4-hydroxychlorothalonil, carbendazim and methoxyfenozide exceeded the PC95 ETV, however no exceedances of the PC95 were observed for dimethoate. The hazard quotient (HQ) method was used to identify high hazard sites across the GBR catchment area. In total, six sites were identified as having concentrations that exceeded the PC95 ETVs. For 4-hydroxychlorothalonil, the risk to aquatic species based on the 95th percentile concentrations ranged from 3 to 13 %, 1 to 8 % for carbendazim and 2 to 8 % for methoxyfenozide. Detected concentrations of carbendazim were two orders of magnitude higher than concentrations that are reported to induce behavioural effects in some fish species. Considering that detected concentrations of three of the four PAIs individually pose a potential risk to aquatic species, their contributions to pesticide mixture toxicity should be further assessed.