The global utilization of medicinal plants is steadily increasing due to their rich repository of bioactive compounds, known as secondary metabolites, which are pivotal in promoting health and treating various ailments. Beyond their traditional use in medicine, these plants play significant roles in culinary arts, food preservation, cosmetic industries, and herbal formulations. However, this growing demand has intensified challenges such as habitat loss, overharvesting, unauthorized cultivation, and the adverse effects of climate change, threatening the sustainability of medicinal plant resources. This chapter explores the innovative role of hydroponics as a sustainable and efficient alternative for cultivating medicinal plants. Hydroponic systems, by allowing precise control over environmental variables, including light intensity, pH, humidity, electrical conductivity, aeration, and nutrient composition-offer significant potential to optimize the yield and consistency of secondary metabolite production. These controlled conditions help overcome the limitations of traditional soil-based agriculture, providing benefits such as increased growth rates, improved biomass accumulation, enhanced resource efficiency, and year-round cultivation. Furthermore, this chapter delves into plant physiology-based approaches to strategically manipulate ambient conditions for stimulating specific metabolic pathways, thereby enhancing the biosynthesis of desirable secondary metabolites. Case studies and experimental insights are discussed to illustrate how hydroponics can be tailored to meet the specific growth and metabolite needs of various medicinal plant species. Overall, this chapter emphasizes hydroponics as a transformative cultivation platform, capable of supporting both the conservation of medicinal plants and the sustainable production of their valuable therapeutic compounds in an ecologically responsible manner.