Chemical pollution was indicated as a global environmental problem since elevated concentrations of toxic substances were recorded in almost all ecosystems worldwide. Trace elements, released to environment due to industrial, agricultural and urban activities, are of special concern due to their non-degradability, persistence, bioaccumulation in organisms and potential toxicity. Reliable methods for assessing the level of pollution are essential for proper monitoring and control of pollution. A useful tool for this purpose is the geochemical background (GB), which enables to differentiate between unpolluted and polluted areas as well as calculate pollution indices. The study presents the first attempt to estimate the background values for aquatic plants using cosmopolitan submerged aquatic macrophyte Ceratophyllum demersum as a model species. Water and plant samples were collected from 117 water bodies. Contents of 15 elements (As, Ca, Cd, Co, Cr, Cu, Fe, K, Li, Mg, Mn, Na, Ni, Pb, V, Zn) were determined using atomic absorption spectrometry and flame photometry. Four methods were tested for estimation of the background concentrations: Median ± 2Median Absolute Deviation, Iterative 2σ technique, Tukey box-plot, Grouping of data with 60 % coefficient of variation (CV). Wide ranges of element concentrations in water and various values of Contamination Factor indicated to a variety of natural and anthropogenic impacts in the studied area, which confirmed that the database covered a real environmental variability. Very different estimates of background concentrations were obtained depending on the method. The highest background values were usually given by Me±2MAD method. Grouping of data with 60 % CV was most exigent in defining a site as undisturbed, therefore this method was recommended as the most suitable for estimation of the background values for C. demersum. Pollution Load Index validated the use of estimated background concentrations as reliable for bioindication of pollution in aquatic reservoirs.