The aim of the study was to explore the role of volatile fatty acids in batch scale anaerobic digestion of two potential aquatic weeds (water hyacinth and salvinia), as substrates for anaerobic digestion. Inoculum (cow dung) to biomass (aquatic weeds) ratio of 0.25:1, 0.5:1, 1:1 and 3 1 were taken and monitored in a 2 L digester for 30 days. The maximum amount of biogas produced for was 406 L kg(-1) VS for water hyacinth in 0.5:1 and 330 L kg(-1) VS for salvinia in 1:1 and 3:1 ratio for both. The total VFA for water hyacinth and salvinia were 410 mg L-1 & 365 mg L-1, 424 mg L-1 & 316 mg L-1, 272 mg L-1 & 234 mg L-1 and 158 mg L-1 & 94 mg L-1 in 0.25:1, 0.5:1, 1:1 and 3:1 ratios respectively. Multiple linear regression was performed to find the relationship between the methane from biogas, total VFA, acetic acid and propionic acid for enhanced biogas production. It was observed that total VFA significantly influenced methane content in 1:1 (SC) and 3:1 (WC).