The present investigation was carried out to understand the proximate composition, and the secondary phytochemical compounds and their metabolites present in algae, spirulina, chlorella and azolla. Spirulina contains a rich source of crude protein (58.94%), followed by chlorella (47.08%) and azolla (21.82%). The content of crude fat was higher in chlorella (5.68%), followed by azolla (4.00%) and spirulina (1.54%). The crude fibre level was found to be higher in azolla (26.21%), followed by chlorella (2.87%) and spirulina (1.00%). The gross energy was higher in chlorella (4,377 kcal/kg), followed by spirulina (4,183 kcal/kg) and azolla (3,295 kcal/kg). The secondary phytochemical analysis revealed presence of alkaloids, terpenoids, flavonoids, tannis, polyphenols, saponins, cardiac glycoside and quinones in these algae at different levels. The GC-MS analysis showed presence of 11 metabolic compounds, of which 5 from petroleum etheric extract and 6 from methanolic extract. The chlorella showed presence of 14 secondary metabolites, of which 5 from petroleum etheric extract and 9 from methanolic extract. In azolla, there were 13 secondary metabolic compounds, of which 6 from petroleum etheric extract and 7 from methanolic extract. Therefore, a total of 38 secondary metabolites, which includes 12 different bioactive principle compounds, were identified in these algae. Docosane was found to be present both in spirulina and azolla. Similarly, Tetradecanoic acid was found to be present both in spirulina and chlorella. The remaining ten bioactive principle compounds are species specific, such as 9-octadecenal; and Hexadecanoic acid are for spirulina, Dodecanoic acid; 6,7-Dimethoxy-2-tetralone; 3,7,11,15-Tetramethyl-2-hexadecen-1-ol; Phenol, 2-methoxy-5-(1-propenyl)-,(E); Cycloheptane,1,3,5-tris(methylene); 4-(6,6-Dimethyl-2-methylenecyclohex-3-enylidene)pentan-2-ol; and Loliolide are for chlorella, and cis-2-[2-(hydroxymethyl)cyclopentyl]ethanol is for azolla. Thus, these algae are rich in natural organic compounds. Their pharmaceutical and nutraceutical potencies need to be studied.