Expansion of sugarcane crops may have contributed to the increased contamination of native habitats in Brazil. Several species of amphibians inhabit ponds formed in flooded farmlands, where pesticide concentrations are usually high. This study evaluated the ecotoxicological effects of the sugarcane pesticides fipronil and 2,4-D, as well as the fertilizer vinasse (isolated and mixed), on physiological responses of Leptodactylus fuscus and Lithobates catesbeianus tadpoles. In situ assays were conducted in mesocosms with concentrations based on the doses recommended by the manufacturer. Vinasse (1.3\% dilution) caused 100\% tadpoles' mortality immediately after its application. Fipronil and/or 2,4-D altered antioxidant and biotransformation responses, induced neurotoxicity and changed lipid contents in tadpoles. A multivariate approach indicated that the mixture of pesticides induced most of the sublethal effects in both tadpole species, in addition to the isolated fipronil in L. fuscus. Fipronil alone increased glucose-6-phosphate dehydrogenase (G6PDH) activity, decreased acetylcholinesterase (AChE) and total lipid contents, and altered some individual lipid classes (e.g., free fatty acids and acetone-mobile polar lipids) in L. fuscus. The interaction between fipronil and 2,4-D in this species were more evident for lipid contents, although enzymatic alterations in G6PDH, AChE and glutathione-S-transferase (GST) were also observed. In L. catesbeianus, the mixture of pesticides reduced triglycerides and total lipids, as well as increased GST and decreased AChE activities. The detoxifying enzyme carboxylesterase was reduced by 2,4-D (alone or in mixture) in both species. Isolated pesticides also modulated specific lipid classes, suggesting their disruptive action on energy metabolism of tadpoles. Our study showed that fipronil, 2,4-D, and vinasse, individually or mixed, can be harmful to amphibians during their larval phase, causing mortality or impairing their functional responses.