Background: Aldrovanda vesiculosa L. is a small aquatic plant that produces snap traps for capturing zooplankton prey. Aldrovanda belongs to the family Droseraceae, which is well known for the production of secondary metabolites (especially naphthoquinones). However, compared to other species in this family (Drosera and Dionaea), A. vesiculosa has been very poorly studied in terms of metabolites. The Aim: To fill this gap in knowledge, we investigated what secondary metabolites are present in the shoots of these plants. A hypothesis was tested stating that there are more metabolites in the younger (apical) parts of the shoots, which protect them from herbivores. Methods: Shoots of A. vesiculosa were collected, and the plant material was extracted with methanol, followed by 80% methanol or pure acetone using the accelerated solvent extraction method. The phytochemical profile was established using UPLC-DAD-(ESI)-MS. Results: A. vesiculosa shoots contained gallic acid and its derivatives, ellagic acid and its derivatives, flavonoids, and naphthoquinones (plumbagin and hydroplumbagin hexoside). A gradient (apical–basal) of gallic acid, ellagic acid, plumbagin, and hydroplumbagin hexoside was observed in the shoots. Meanwhile, the total flavonoid content did not differ between the middle and apical parts but was significantly lower in the basal part. In general, the lowest concentrations of metabolites were found in the basal part and the highest in the apical part, with the exception of total flavonoids. The number of free flavonoid aglycones was significantly higher in the middle part, whereas the apical part was dominated by glycoside derivatives.