Flooding is becoming more frequent and severely affects agricultural production, however, compared to other stressors in plants, the underlying stress management mechanisms are largely underexplored. Using chromatographic (GC-MS, LC-MS) and spectrophotometric analyses, we assessed the impact of long-term (i.e., 24 days) waterlogging on seven Brassica oleracea varieties that belong to different vegetable forms. The response of the metabolism was analysed by assessing the levels of phytohormones, polyphenols, and glucosinolates, and was linked with the impact on stress biomarkers and antioxidative systems. The major outcome of this research is the observed high variety-specific response to waterlogging. Savoy cabbage displayed more severe alterations in its specialised metabolism, which may have been mediated by indole-3-acetic acid (IAA). The expression of the corresponding biosynthesis genes was shown to be linked with changes in metabolic parameters. Modifications in phenolic metabolism pathways affected the antioxidative capacity and potentially influenced the gene expression of genes encoding antioxidative enzymes. The variable effects of waterlogging may indicate the potential of certain specialised metabolite groups as biomarkers for such stress conditions in Brassica plants that can be used to guide future agricultural practices. Furthermore, new insights into the underlying processes of waterlogging stress could aid future studies aimed at strengthening plant stress resilience in the era of severe climate change.