2-chloro-3-(4-methylpiperazin-1-yl)naphthalene-1,4-dione (3a), 2-chloro-3-(pyrrolidin-1-yl)naphthalene-1,4-dione (3b), 2-chloro-3-(piperidin-1-yl)naphthalene-1,4-dione (3c), 2-chloro-3-morpholinonaphthalene-1,4-dione (3d), 2-chloro-3-(2-phenylhydrazinyl)naphthalene-1,4-dione (3e), 2-(allylamino)-3-chloronaphthalene-1,4-dione (3f), 2-(3-chloro-1,4-dioxo-1,4-dihydronaphthalen-2-ylthio)acetic acid (3g), 2-(3-chloro-1,4-dioxo-1,4-dihydronaphthalen-2-ylthio)succinic acid (3h), methyl 2-(3-chloro-1,4-dioxo-1,4-dihydronaphthalen-2-ylthio)acetate (3i), 2-chloro-3-(2-mercaptoethylthio)naphthalene-1,4-dione (3j), 3-hydroxy-4-methyl-4H-naphtho[2,3-b][1,4]thiazine-5,10-dione (3k) and compounds 3l-q have been synthesized by a green methodology approach using water as solvent and evaluated for their antifungal and antibacterial activity. The antifungal profile of 3a-n indicated that compounds 3a-d, 3j, 3e and 3k have potent antifungal activity. Amongst the most promising antifungal compounds, 3a-g, 3j, 3k showed better antifungal activity than clinically prevalent antifungal drugs Fluconazole and Amphotericin-B against Trichophyton mentagraphytes and compounds 3j and 3k have been found to be lead antifungal bicyclic and tricyclic 1,4-naphthoquinones. Compound 3k also exhibited pronounced antibacterial activity.