Water hyacinth is a non-edible plant having a severe impact on aquatic ecosystems through native vegetation displacement and lower dissolved oxygen concentration. High cellulose and low lignin content make water hyacinth a potential source for biofuel production. Water hyacinth was subjected to acid pretreatment using organic acids (citric acid (CA) and oxalic acid (OA)) and mineral acid (hydrochloric acid (HA)) to enhance enzymatic saccharification, and ethanol and biogas production. Under optimized pretreatment condition, the reducing sugars released from enzymatic saccharifications of CA-, OA-, and HA-pretreated samples increased by 2.56-, 1.71-, and 1.62-fold, respectively, than untreated sample. Maximum ethanol yield (8.97 g/L) was observed for OA-pretreated (1.68-fold increase) than untreated water hyacinth, whereas CA-pretreated sample produced the highest biogas yield (3421.5 mL) after anaerobic digestion for 45 days. The increase in the yield of ethanol and biogas for OA and CA is attributed to the changes in the hemicellulose and lignin structure. The change in the structural morphology was observed through FTIR characterization of untreated and treated water hyacinth. In addition, the effect of post-washing after pretreatment on fermentation efficiency was evaluated and the result suggested that CA residues had no negative effect on ethanol production. Pretreatment of water hyacinth using organic acids could benefit the biorefineries through the biofuel production and reduction of wastewater generated from this process. © 2022, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.