An analytical method for the quantification of the widely used herbicide, glyphosate, its main by-product, aminomethylphosphonic acid (AMPA) and the herbicide glufosinate at trace level was developed and tested in different aqueous matrices. Their derivatization with 9-fluorenylmethyl chloroformate (FMOC-Cl) was done prior to their concentration and purification by solid phase extraction. The concentrated derivates were then analyzed by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Spiking tests at three different concentrations were realized in several water matrices: ultrapure water, Evian© mineral water, river water, soil solution and runoff water of a vineyard. Except for AMPA in runoff water, obtained regression curves for all matrices of interest showed no statistical differences of their slopes and intercepts, validating the method for the matrix effect correction in relevant environmental samples. The limits of detection and quantification of the method were as low as 5 and 10 ng/l respectively for the three compounds. Spiked Evian© and river water samples at two different concentrations (30 and 130 ng/l) showed mean recoveries between 86 and 109%, and between 90 and 133% respectively. Calibration curves established in spiked Evian© water samples between 10 and 1000 ng/l showed r2 values above 0.989. Monitoring of a typical vineyard river showed peaks of pollution by glyphosate and AMPA during main rain events, sometimes above the legal threshold of 100 ng/l, suggesting the diffuse export of these compounds by surface runoff. The depth profile sampled in the adjacent lake near a waste water treatment plant outlet showed a concentration peak of AMPA at 25m depth, indicating its release with treated urban wastewater.