A method for the identification and quantification of neutral diphenyl-ether (DPhE) (aclonifen, bifenox, fluoroglycofen, lactofen, oxyfluorfen) and acid metabolites (acifluorfen, bifenox acid, fomesafen) at a low nanogram per liter concentration level in natural water is presented. These herbicides and their metabolites were determined in drinking water, groundwater, and river water. The analytes were isolated from water samples by solid-phase extraction (SPE) on Carbograph-1 cartridges and analyzed with reversed phase high-performance liquid chromatography (RP-HPLC) using UV detection at a wavelength of 290nm. The isolation procedure separated the acid DPhE from neutral DPhE during the elution from Carbograph-1 cartridge using dichloromethane:methanol (80:20, v/v) for neutral compounds and dichloromethane:methanol (80:20, v/v) acidified with 25mmol/l of formic acid for the anionic metabolites. Quantification was performed by generation of an external calibration curve. High recoveries (>85%) of extraction were obtained for all the compounds. The method detection limit ranged from 4.1 to 8.7ng/l for drinking water, from 5.1 to 9.5ng/l for groundwater and from 17.5 to 36.2ng/l for river water. This method involves confirmatory analysis by tandem mass spectrometry (MS-MS) in selected reaction monitoring (SRM) mode. Conditions for MS-MS detection of characteristic daughter ions formed by collision-induced dissociation of the parent ion are described. The final samples were analyzed by HPLC-MS-MS utilizing a heat-assisted electrospray interface (turbo ion spray) (TISP) for acid DPhE and a heated nebulizer (HN) interface for neutral DPhE. Quantification was performed by generation of an internal calibration curve. Excellent method precision was demonstrated with a relative standard deviation of less than 18% for all analytes at all concentration levels. Application of the method for detecting DPhE herbicide residues in a real-world groundwater samples was demonstrated.