Microcystin-LR (MC-LR) as a drinking water contaminant was degraded using iron-based nanoparticles such as nZVI, Fe/Ni and Fe/Pd. Batch experiments showed that 28.0% of MC-LR with the initial concentration of 5mgL−1 was removed using nZVI, while more than 90% of MC-LR was removed using either bimetallic Fe/Ni or Fe/Pd after degrading for 120min. In addition, the results indicated that Fe0 was oxided to iron oxide or hydroxide after reacting with MC-LR, while Ni or Pd acted as the catalysis to prevent Fe0 corrosion and generating hydrogen via water reduction. Degradation of MC-LR by iron-based nanoparticles fitted well to the pseudo-first order kinetic model and the degradation was a diffusion-controlled reaction with low activation energies (8–21kJmol−1). Finally, the degradation mechanisms of MC-LR using iron-based nanoparticles were proposed according to the LC–MS analysis. In nZVI case, when the MC-LR was quickly adsorbed on nanoparticles, electron transfer and H2 generated from iron corrosion were generated and broke down the Adda composition of MC-LR. Based on corrosion in the Fe0–H2O system, bimetallic Fe/Ni and Fe/Pd further utilized the abundant hydrogen radical decomposed from H2 under the catalysis of Ni or Pd, and destroyed the Adda to form small molecules.