Pesticides used in agriculture are widely considered to be the most cost-effective way to reduce undesirable plants and animal pests and increase crop yields. However, these economic benefits should be evaluated against any deleterious impacts on the natural environment and human health. While a great deal of attention is paid to the impact of agricultural runoff, more studies are needed on the impacts of pesticides on local waterways. The aim of this study was to: (i) develop a methodology to determine which pesticides were being used in local agriculture in the Byron Shire, Australia, and (ii) search the literature for evidence of the impact of these chemicals on local waterways. After a comprehensive search involving multiple government databases, three herbicides with potentially high toxicity on the aquatic ecosystems and humans, which are used for the treatment of crops cultivated on the agricultural land in the Byron Shire, Australia, were selected for this review: bromoxynil, diquat and paraquat. In the systematic scoping review, two databases were searched (Scopus and Web of Science) for publications between January 2008 and April 2019. From 160 articles identified, 36 papers were selected for inclusion. The evidence of harmful effects at realistic field concentrations (concentrations that are within the recommended safety range for use in the environment) was found for all selected herbicides, but not on all organisms. In aquatic environments, diquat was found to be toxic to snails and bromoxynil to microalgae. The clearest and most consistent evidence was found for paraquat. At realistic field concentrations, paraquat: (i) severely inhibited healthy bacterial growth (E. coli), (ii) distorted tropical freshwater plankton communities, and (iii) increased fish kills (common carp) three times more than the weed (water hyacinth) that it was employed to control. Of particular concern is that paraquat has been banned from sale in the European Union and many countries around the world but remains available in Australia and is likely in use in the Byron Shire. While there are existing Australian government regulations restricting the use of paraquat in agriculture, further work is required to scope the extent of its use, the effectiveness of these regulations and the amount of paraquat entering the environment. This study provides a methodology that can be used to identify pesticides that are likely to be in local use and to identify evidence of any negative impacts on the health of local waterways.