The abundance of toxic contaminated effluents from the pharmaceutical industries and the serious risk of contamination of the aquatic systems combine to provide strong motivating factors to tackle this environmental problem. Use of non hazardous chemicals, reaction in aqueous medium is an interesting ecological alternative for the bulk production of important drugs and fine chemicals. Taking advantage of the remarkable ability of the selected catalytic systems, alternative sustainable methods have been exploited for the decontamination of industrial effluents and exhausts. Working in the same direction herein, we present a newly developed metal-organic complex [Bis(picolinate-κ2N:O) Cu(II)] catalysed A3-coupling reaction in water which has established an excellent greener protocol to yield propargylamine. Low toxicity, easy access to active sites, high surface area, high thermal stability, recyclability of the catalyst and easy way to separate the catalyst from the reaction mixture are the added advantage of this developed greener and sustainable protocol.