The effect of disturbed root nodulation on the quantitative and qualitative composition of the main isoflavonoid glucoside malonates, glucosides, and aglycones in the leaves of Trifolium pratense L. grown under waterlogging conditions was investigated. Isoflavonoids are involved in the regulation of root nodule activity and the establishment of the mycorrhizal association. Isoflavonoid determination was performed using reversed-phase liquid chromatography coupled to mass spectrometric and UV absorbance detection. In response to waterlogging, the concentrations of biochanin A and biochanin A-7-O-glucoside malonate, biochanin A-7-O-glucoside, and genistein-7-O-glucoside in the leaves increased two- to threefold after a lag period of 3 wk because of disturbed root nodulation. The other isoflavones detected formononetin, formononetin-7-O-glucoside malonate, and formononetin-7-O-glucoside-did not show any significant changes related to waterlogging. After restoring normal soil water conditions, the concentrations of biochanin A and its glucoside and glucoside-malonate rapidly returned to the initial values, whereas the concentration of genistein-7-O-glucoside remained high.