The aim of this study was to produce optimal wastewater treatment solutions to calculate the removal of different contaminants of emerging concern (CECs) found in developing countries. A new methodology was developed for a decision support tool (WaStewater Decision support OptiMiser, WiSDOM), which focuses on producing treatment solutions suited to treating water for reuse to Indian Water Quality Standards. WiSDOM-CEC analyses the removal of CECs through different treatment solutions and was also used to evaluate the performance of each treatment train solution in terms of the removal of conventional pollutants using multi-objective optimisation and multi-criteria decision analysis. Information was collected on different CECs across different regions of India, and the removal of 18 different CECs through 42 wastewater treatment unit processes for five different regions of India was analysed. Comparisons between similar categories of CECs, such as non-steroidal anti-inflammatory, showed that emerging contaminants all react differently with individual treatment options. For example, the removal of ibuprofen (IBP) and naproxen (NPX) varied from >80% and 0%, respectively, for a solution in Karnataka involving sedimentation, submerged aerated filter, ultrafiltration and nanofiltration. In Tamil Nadu, results ranged from 36.8% to 72% for diclofenac, 10.7% to 66.5% for IBP, and 0% for NPX.