Synthesis of a series of tri-substituted methane derivatives has been reported via a one-pot multicomponent reaction of aldehyde, 1,3-dimethyl-6-aminouracil and 2-hydroxy-1,4-naphthoquinone/4-hydroxycoumarin using a bifunctional thiourea-based organocatalyst in aqueous medium. Use of the organocatalyst, and water as a solvent, without the need for column chromatographic purification, are the notable features of this methodology.