Residues of glyphosate (GlyP) and its major degradation product, aminomethylphosphonic acid (AMPA), widely exist in the water system and plant products and thus are also present in the bodies of animals and humans. Although no solid evidence has been obtained, the concern about the cancer risk of GlyP is persistent. The measurement of GlyP and AMPA in trace levels is often needed but lacks readily available analytical approaches with detection sensitivity, accuracy and speed. This study aims to develop a simple and robust technique for the sensitive detection of GlyP and AMPA residues in a surface water system with flow-gated capillary electrophoresis (CE). Experimentally, water samples were first fluorogenically derivatized with 4-fluoro-7-nitrobenzofurazan (NBD-F) in a low-conductivity buffer at room temperature, and the mixture was injected and concentrated in the capillary based on field-amplified sample injection (FASI) coupled with electrokinetic supercharging (EKS). This scheme included a step of sample buffer injection upon electroosmotic pumping, where negatively charged analytes were electrophoretically rejected, followed by automatic voltage reversal for FASI-EKS. The detection sensitivity was improved by 296, 444, and 861 times for glufosinate (GluF), AMPA, and GlyP, respectively. The proposed method was validated in terms of accuracy, precision, limits of detection (LODs), and linearity. The LODs were estimated to be 50.0 pM, 5.0 pM, and 10.0 pM for GluF, AMPA, and GlyP, respectively. Its application was demonstrated by measuring GluF and AMPA in water samples collected from a local water system. This study provides an effective approach for the online preconcentration of negatively charged analytes, thus enabling the sensitive detection of herbicide residues in water samples. The method can also be applied to analyze other samples, including biological fluids and plant products, upon appropriate sample preparation such as solid phase extraction of analytes.