Organic Medium Enclosed Trough (OMET) system is a new non-drainable growing technique. The study set out to investigate the interactive effects of OMET and Amaranth species variation on some growth attributes, yield, bioactive compounds, and nutrients. Three Amaranth species, A. caudatus, A. cruentus, and A. tricolor, were grown in OMET and non-OMET growing conditions. Growth attributes, irrigation water, bioactive compounds, and nutrients were determined. Non-OMET growing conditions and A. cruentus showed the highest total phenolics and flavonols followed by A. caudatus and A. tricolor, whilst tannins were predominant in A. caudatus followed by A. cruentus and A. tricolor. The use of unsupervised PCA showed major metabolic variation based on Amaranth species and the use of supervised OPLS-DA showed clear metabolic variation based on OMET and non-OMET. OMET and A. cruentus showed the highest plant height, stem diameter, biomass, and some nutrients (%protein, Ca, P, Cu, Se, Zn), followed by A. caudatus based only on growth and biomass, and A. tricolor based only on some nutrients (Mg, K, Mn, and Fe). The use of the OMET system on A. cruentus and A. tricolor can be recommended to mitigate climate change effects on nutritional composition using relatively low levels of irrigation water.