There has been a rapid increase in the number of pesticides and there is limited information on the effects of these new pesticides on aquatic ecosystems. Few new pesticides are routinely included in environmental studies, therefore their presence in the environment may go undetected. Furthermore, ecotoxicological studies of these pesticides are conducted on a small number of laboratory species, so it is questionable whether all ecological values will be adequately protected. This study aimed to develop a simplistic methodology to identify emerging pesticides of potential concern within a local region that pose a threat to local ecological values. The greater Melbourne area (GMA) was used as a model for this study and the regional aquatic ecological values were identified. Pesticides registered for use in the GMA within the past decade were identified and those pesticides not being routinely tested by major Australian analytical laboratories were shortlisted. Ecotoxicity data for local aquatic ecological values were used to assess and prioritise pesticides based on acute and chronic toxicity. A list of 143 pesticides was shortlisted from approximately 4,000 compounds that are registered and approved for use within the GMA. The limitations in the existing Australian guidelines for the regulation of pesticides in environmental water systems are discussed. The lack of information on some agrochemical classes such as rodenticides and parasiticides indicated the need for improving local monitoring studies within aquatic systems. There is a need for more ecotoxicological studies on the effects of emerging pesticides on endemic Australian amphibians and the platypus. Different emerging pesticides of concern are likely to be identified in other regions of the world as they will have different ecological values to those identified in the GMA. This approach can assist authorities in the regulation of emerging pesticides that could potentially threaten aquatic systems.