Herbicides glyphosate (N-(phosphonomethyl)glycine) and glufosinate (2-amino-4-(hydroxymethylphosphinyl)butanoic acid) and the main transformation product of glyphosate, aminomethanephosphonic acid (AMPA), are challenging to analyze for in environmental samples. The quantitative method developed by this study adapts previously standardized dechlorination procedures coupled to a novel charged surface C18 column, ultra-high performance liquid chromatography-tandem mass spectrometry, polarity switching, and direct injection. The method was applied to chlorinated tap water, as well as river samples, collected in the City of Winnipeg and rural Manitoba, Canada. Using only syringe filtration without derivatization, the validated method resulted in good accuracies in both tap and surface water, at both 2 and 20 μg L−1. Method limits of detection (MLD) and quantification (MLQ) ranged from 0.022/0.074 to 0.11/0.36 μg L−1, with precisions of 0.46–2.2% (intraday) and 1.3–7.3% (interday). The mean (SEM) of the pesticides in μg L−1 for tap water were 0.11 (0.007) (AMPA), glufosinate and glyphosate < MLDs; and for Red River water were 0.56 (0.045) (AMPA), glufosinate < MLQ, and glyphosate 0.40 (0.072). For the smaller tributaries, glufosinate was >MLD but < MLQ once and that was for Shannon Creek at 0.2 μg L−1. For the remaining rivers, the mean concentrations ranged from 0.31 to 3.1 μg L−1 for AMPA, and 0.087–0.53 μg L−1 for glyphosate. The method will be ideal for supporting monitoring and risk assessment programs that require high throughput sampling and quantitative methods capable of producing robust results that leverages chromatographic and mass spectrometric paradigms instead of being extraction technology focused.