Six naturally occurring minerals were employed to catalyze the hydrolysis of microcystin-LR (MC-LR) in water. After preliminary screening experiments, siderite stood out among these minerals due to its higher activity and selectivity. In comparison with kaolinite, which is known to act as a Lewis acid catalyst, siderite was found to act primarily as a Brönsted acid catalyst in the hydrolysis of MC-LR. More interestingly, we found that the presence of humic acid significantly inhibited catalytic efficiency of kaolinite, while the efficiency of siderite remained high (∼98%). Reaction intermediates detected by LC-ESI/MS were used to indicate cleavage points in the macrocyclic ring of MC-LR, and XPS was used to characterize siderite interaction with MC-LR. Detailed analysis of the in situ ATR-FTIR absorption spectra of MC-LR indicated hydrogen bonding at the siderite-water-MC-LR interface. A metastable ring, involving hydrogen bonding, between surface bicarbonate of siderite and an amide of MC-LR was proposed to explain the higher activity and selectivity toward MC-LR. Furthermore, siderite was found to reduce the toxicity of MC-LR to mice by hydrolyzing MC-LR peptide bonds. The study demonstrates the potential of siderite, an earth-abundant and biocompatible mineral, for removing MC-LR from water.