Rapid and highly efficient one pot green chemical synthesis of substituted 6-(2-aminophenyl)-4-(4-substitutedphenyl)-3-thioxo-3,4-dihydro-1,2,4-triazin-5(2H)-one and 8-substituted-3,5-dihydro-2H-[1,2,4]triazino[5,6-b]indole is carried out in aqueous medium under microwave irradiation. Improved synthesis of potent bioactive Schiff and N-Mannich bases of hexahydro-1H-indole-2,3-dione is also reported. The title compounds are easily accessible by various approaches; even waste free approaches have been developed. The operational simplicity, environmentally benign conditions and high yield achieved in a very short reaction time are major benefits that meet the requirements of green production, including saving energy and high efficiency. The results obtained under microwaves are compared with that of conventional heating. Structural assignments are based on spectroscopic data. Compounds have also been screened for antibacterial and antifungal activities.