A method based on Immobilised Metal Ion Affinity Chromatography (IMAC) using a chelating resin (Spheron Oxine 1000) loaded with Pd(II) is evaluated for the extraction and preconcentration of glyphosate and AMPA from natural water samples. The efficiency of the metal-loaded resin in retaining glyphosate and AMPA and the ability of different reagents to recover them is investigated. The most effective elution solution for the recovery of both analytes from the resin is found to be a mixture of 0.1 M HCI and 1 M NaCl. The effect of flow rate, analyte concentration, and sample volume is evaluated. The optimised experimental conditions are then used in the extraction of the analytes from spiked natural waters. The use of the Pd loaded resin led to recoveries ranging from 80-90% for glyphosate and 60-80% for AMPA.