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Medicinal aromatic plants (MAPs) are cultivated for the production of specialty materials including essential oils (EO), and pharmaceuticals, but most are still wild collected. The need for renewable sources of intensive industrial products as well as the protection of plant biodiversity can be satisfied by cultivating MAPs as agro-industrial crops. Such crops require ample amounts of irrigation water to meet their potential for rigorous production. Shortage of fresh water in arid and semi-arid zones has necessitated the development of MAPs production systems based on irrigation with treated effluents. In the present study we have investigated the MAP Clinopodium serpyllifolium for its suitability to grow under irrigation with treated effluents, as a source of EO and pharmaceuticals. The results have demonstrated the suitability of the utilization of treated effluents for agro-industrial production of C. serpyllifoliwn, as a promising source of high quality EO, and biomass production, without compromising yield parameters and bioactivities, compared with potable water irrigation. The results indicate that C. serpyllifolium is a valuable natural source of antioxidants and cholinesterase inhibitors, with interesting inhibitory actions against the key enzymes involved in Alzheimer’s disease (AD) and could represent a starting point for the development of new AD management strategies using natural butyrylcholinesterase inhibitors, including its use as a food supplement. The study has demonstrated the ability of C. serpyllifolium extracts to exert health benefits by inhibiting pancreatic lipase, a target for obesity. Treated effluents is suitable for growth and quality production in C. serpyllifolium, and hence it forms the foundation for effluent-based industrial EO production.