A chromatographic-mass spectrometric study of the low molecular weight metabolome (LMWM) of water smartweed (Persicaria amphibia (L.) Delarbre, family Polygonaceae Juss.), growing in various biotopes of Lake Ladoga, was carried out for the first time during the flowering phase in order to reveal its qualitative and quantitative composition. Essential oil containing low molecular weight organic compounds (LMWOC) from dried plants was obtained by Clevenger hydrodistillation with steam. The composition and content of LMWOC in the essential oil were detected using a TRACE DSQ II chromato-mass spectrometric complex (Thermo Electron Corporation) in a programmed temperature mode using decafluorobenzophenone and benzophenone as internal standards. A total of 124 LMWOC were detected, of which 110 were identified. Carboxylic acids (50–60 % by content), aldehydes (9–14 %) and hydrocarbons (6-9%) prevailed among the LMWOC in the water smartweed. The LMWM of P. amphibia from the biotope exposed until recently to heavy human impact (effluents from the pulp and paper industry and woodworking enterprises) featured the smallest number of LMWOC (87 versus 107 and 114 in other biotopes), and their total content was 3–3.5 times lower than in plants growing under more favourable conditions. The presence of a number of biologically active metabolites in the LMWM of water smartweed suggests this plant has a pronounced effect on littoral aquatic organisms communities in Lake Ladoga.