The typical time-dependent decrease of the iron corrosion rate is often difficult to consider while designing Fe0-based remediation systems. One of the most promising approaches is the amendment with manganese dioxide (Fe0/MnO2 system). The resulting system is a very complex one where characterization is challenging. The present communication uses methylene blue discoloration (MB method) to characterize the Fe0/MnO2 system. Shaken batch experiments (75 rpm) for 7 days were used. The initial MB concentration was 10 mg L−1 with the following mass loading: [MnO2] = 2.3 g L−1, [sand] = 45 g L−1, and 0 < [Fe0] (g L−1) ≤ 45. The following systems where investigated: Fe0, MnO2, sand, Fe0/MnO2, Fe0/sand, and Fe0/MnO2/sand. Results demonstrated that MB discoloration is influenced by the diffusive transport of MB from the solution to the aggregates at the bottom of the test-tubes. Results confirm the complexity of the Fe0/MnO2/sand system, while establishing that both MnO2 and sand improve the efficiency of Fe0/H2O systems in the long-term. The mechanisms of water decontamination by amending Fe0-based systems with MnO2 is demonstrated by the MB method.