Abstract <p>A chromatograph mass spectrometric study of the essential oil of the yellow water lily (<i>Nuphar lutea</i> (L.) Sm.) growing in Lake Kuznechnoye in Leningrad oblast on the Karelian Isthmus was carried out at the peak of plant development in the flowering–fruiting phase in 2020 and 2021 for the first time. The goal is to study the interannual variability of the component composition of low-molecular-weight organic compounds (LMWOCs) and assess the possibility of using its low-molecular-weight metabolome (LMWM) to indicate the ecological state of water bodies. The limnological characteristics of the water body in the place where the yellow water lily grows are given. The main research method of the work is gas chromatograph–mass spectrometry (GC–MS). It is revealed that, under changing environmental conditions in different years, including depending on a specific biotic environment (phytoplankton) and abiotic factors, plants are able to synthesize different numbers of LMWOCs. The decrease in the trophic status of the lake ecosystem and the decrease in the development of cyanobacteria, as the dominant component of phytoplankton, leads to a significant increase in the content of all groups of components in the LMWM of the yellow water lily. The intraspecific interannual variability of the LMWM of the yellow water lily can serve as an indicator of stability/changes in the state of the aquatic ecosystem. The high quantitative indicators of LMWOC content, especially allelochemical substances, identified in <i>N. lutea</i> from Lake Kuznechnoye, typical for the Karelian Isthmus, indicate that the yellow water lily growing in the lakes of the Karelian Isthmus is an underutilized natural resource of valuable LMWOC with the potential for diverse economic use.</p>