Novel SO₃H-functionalized ionic liquids bearing two alkyl sulfonic acid groups in the imidazolium cations were designed and successfully applied as catalysts for the one-pot Fischer indole synthesis in water medium. The sequence of the catalytic activity observed in the transformation was in good agreement with the Brønsted acidity order determined by the Hammett method. Various types of indoles from single-carbonyl ketones/aldehydes and cyclohexandiones were provided in 68–96% yields using the catalytic system of [(HSO₃-p)₂im][HSO₄]/H₂O. The indole products could be conveniently separated from the reaction mixture by filtration and the dissolved catalyst could be regenerated by treatment with a strongly acidic cation exchange resin, which meant the whole process was performed in water without using any organic solvents.