Veterinary medicinal products are applied in aquaculture production for treating and preventing diseases in the cultured species. Veterinary medicines may enter the environment by effluent discharges, posing a potential risk for surrounding aquatic ecosystems. Furthermore, human health and the trade of the aquaculture produce can be negatively affected by the presence of residues of veterinary medicines in the cultured organisms. The ERA-AQUA Decision Support System was developed to estimate risks of veterinary medicinal products applied in pond aquaculture for the targeted produce, surrounding aquatic ecosystems, consumers and trade. The risk assessment is expressed by risk quotients, which are calculated by dividing the predicted exposure concentration by the predicted no effect concentration calculated for each endpoint. This report provides a mathematical description of the processes incorporated in the ERA-AQUA Decision Support System and a user’s manual.