Cultivated carrot is one of the most important vegetable plants in the world and favored by consumers for its typically sweet flavor. Unfortunately, the attractive sensory quality is hindered by a sporadic bitter off-taste. To evaluate the influence of the abiotic stress conditions, waterlogging and drought, on the bitter sensometabolome as well as agronomical traits of six genotypes of Daucus carota, a field trial was performed. Enabling the accurate tracing of carrots’ bitter compounds and therefore their metabolic changes, a fast and robust high-throughput UHPLC-MS/MS was developed and validated. Remarkably, the genotypes are the driving source for the biological fate of the bitter metabolites that are reflected in concentrations, dose-over-threshold factors, and fold changes. A certain influence of the irrigation level is observable but is overruled by its cultivar. Therefore, metabolic stress response in carrots seems to be genotype dependent. Hence, this study might help to plant specific carrot genotypes that are adapted to stress conditions evoked by future climatic changes.