The aim of this work was to develop a sequential injection (SI) method for the determination of the micronutrients iron and manganese, in soil leachates, as a tool to assess potential groundwater contamination. The described sequential injection method was based on the reaction of iron with chelator MRB12, a greener alternative chromogenic reagent, and the reaction of manganese with zincon, within a single manifold. The developed SI method enabled the determination of iron in the range 0.10-1.00 mg L-1, and manganese in the range 0.25-2.5 mg L-1 with a limit of detection of 0.08 mg L-1 for iron and 0.24 mg L-1 for manganese. The determination of both parameters was made in 6 minutes, in triplicate. The application to monitor laboratory scale soil core columns (LSSCs), as a simulation of the soil leaching process, proved its efficiency to assess potential contamination of ground waters. Iron and manganese contents were effectively analysed in two different scenarios to mimic the leaching process with rainwater and fertilizer.