Pesticides applied to agricultural land have been shown to decrease the quality of water entering the Great Barrier Reef lagoon. This issue is addressed by the Reef 2050 Water Quality Improvement Plan which includes a pesticide reduction target. As part of a wider educational strategy, one method that could help meet the target is to provide stakeholders with information that assists in the selection and use of pesticide active ingredients (PAIs) that pose a lower risk to aquatic environments compared to those currently used. This study developed a Pesticide Decision Support Tool (PDST) in collaboration with stakeholders for the sugar cane industry. The PDST covers all PAIs registered and applied to sugar cane in Australia and four additional PAIs registered for use on crops grown in rotation with sugar cane. The PDST incorporates both the measure of mobility and persistence of a PAI and the measure of effect, which is based on the PAI application rate and ecotoxicity threshold value. The aquatic risk, which is the product of the measure of effect and the measure of mobility and persistence, is a measure of the likelihood that a PAI will reach the aquatic environment and cause harmful effects. Insecticide active ingredients (e.g., cadusafos, chlorpyrifos) posed the greatest aquatic risk, followed by herbicide active ingredients (e.g., MSMA, metolachlor), while fungicide AIs typically had a lower aquatic risk. An interactive spreadsheet allows characteristics, including application rate and tank mixes, to be considered when assessing the potential risk. While focusing on sugar cane, the results are equally appropriate to other crops that use the same PAIs provided the application rates are corrected to the new crop. In addition, the approach used in the PDST can be applied internationally and to any PAIs with sufficient toxicity, mobility, and persistence data.