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Pesticide monitoring programs are required to understand pesticide contamination in the environment. They can be used to compare existing water quality guidelines and associated their presence with activities related to catchments. Thus, provide crucial information for management actions. A major challenge with such programs is to determine which pesticides should be screened and this determination is made more difficult as many new pesticides are continuously emerging on markets. We have developed a robust method to identify those pesticides which should be included in screens based on whether they are likely to be used within the region surveyed and if they pose a threat to aquatic ecosystems. This approach is illustrated by comparing the Warrnambool South West (WSW) and Mornington Peninsula (MP) regions within Victoria, Australia that have contrasting land-use practices. Pest control products registered and approved for land-use activities within the two regions during the past decade were identified using a government database. Those pesticides in these products which were not screened by commercial laboratories were then identified. Region-specific identification of prevalent pesticide usage was estimated by matching the highest-grossing agricultural commodities within the two regions with pesticide-specific land-uses. A total of 56 (WSW) and 54 (MP) unique pesticides and another 34 being common in both regions were identified that can be augmented to standard screens of analytical laboratories. Different pesticides of concern are likely to be identified for aquatic ecosystems in other regions of the world; as they will have different regional land-uses, laboratory screens and different pesticide use to those identified in this study. The approach presented here can assist authorities in identifying which pesticides should be incorporated into local pesticide monitoring programs.