Insecticides such as pyrethroids and organophosphates are extensively used globally. Once released into surface water bodies, they can pose a major threat to aquatic ecosystems already at trace concentrations. Therefore, selected pyrethroids and organophosphates are listed as priority substances within the European Water Framework Directive with chronic quality criteria in the picogram per liter range. Previously applied analytical methods were unable to detect pyrethroids and organophosphates at ecotoxicological relevant concentrations, thereby hindering the assessment of surface water quality. In this work, we developed an ultra-sensitive method for the analysis of 12 pyrethroid and two organophosphate insecticides in surface waters. This method is based on the liquid–liquid extraction of surface water samples with n-hexane to achieve large enrichment factors (4000×) and subsequent chemical analysis by gas chromatography coupled to tandem mass spectrometry using atmospheric pressure chemical ionization, a soft ionization technique. Quality control parameters including the method limits of quantification (12.5–125 pg L−1), intra-day precision (1–22%), intra-day accuracy (84–133%), and absolute recoveries covering liquid–liquid extraction (67–114%) showed that the method is sensitive and robust and therefore suitable for the analysis of pyrethroids and organophosphates in surface waters. The developed method was applied to Swiss surface water samples and detected pyrethroids and organophosphates below the ecotoxicological relevant concentrations, exemplifying the suitability of the proposed method for aquatic monitoring.