We report here a highly efficient green approach for the synthesis of imidazolidin-2-ylidene-indenedione, pyrimidine-2-ylidene-indenedione and indenoquinoxaline derivatives through the one-pot three-component reaction between ninhydrin, malononitrile and various diamines in water medium under catalyst-free conditions. High yields (73–98%) of the target products were achieved with short reaction times at room temperature. Simple workup, no column chromatography, good to excellent yields, rapid reaction and green solvent are the prominent advantages of this protocol.