The presence of human pharmaceutical compounds in surface waters is an emerging issue in environmental science. Low levels of many active pharmaceutical ingredients are detected in the aquatic environment as a result of pharmaco-chemical industrial waste spill-offs in draining water. In the manufacturing of pharmaceutical drug substances azides are used as reagents or when they are generated somehow in the synthesis, it may be necessary to demonstrate that these impurities are sufficiently removed to levels below an appropriate safety threshold. Sodium azide is an example of an azide for which the environmental exposure limits have been reasonably well characterized. The treatment of waste and industrial water can be conducted by removing dissolved materials and ions in water using membrane separation technology with ultra- and nanofiltration (NF) and reverse osmosis (RO) membranes. To achieve better effluent water quality, tertiary treatment with activated carbon adsorption is used. To analyze the risk of pharmaceuticals in the environment, a proposed validated methodology by NMR spectroscopy will support the evaluation of the eco-toxicological hazards during the early development process of pharmaceuticals.