Calcium (Ca) and magnesium (Mg) are vital elements for the neutralization of soil or water acidity, which is associated with the activity of biota, mobility of heavy metals, phosphorus and other important elements. The current research was aimed to estimate the trends in the fluctuation of calcium and magnesium ions in the floodwater using traditional experimental methods. The studies were carried out during the 1987-2010 period in the Nemunas lowland (upper (Rambynas-Plaškiai) and lower (Girininkai-Smalkai) zones) and in the Minija lowland. In the floodwater of both rivers, the concentration of Ca 2+ was up to three times as high as the mean annual concentration in the river and that of Mg 2+ concentration by up to 1.6 times higher than in the river. A trend towards increasing of these ions concentration in the floodwater was established. In the upper zone of the Nemunas lowland the concentrations of Ca 2+ (159-248 mg l -1 ) and Mg 2+ (14.3-29.3 mg l -1 ) in floodwater were something higher than those in the lower zone -152-240 and 13.5-25.3 mg l -1 , respectively. These differences were significant: Ca 2+ -t act. = 1.75 > t 0.05 = 1.65 and Mg 2+ -t act. = 3.25 > t 0.05 = 1.65. The concentration of these ions with increasing distance from the riverbed decreased and was the lowest in the pre-land part of the floodplain. The strongest correlation between Ca 2+ (r 2 = 0.82, t act. = 7.87 > t 0.05 = 1.75) and Mg 2+ (r 2 = 0.43, t act. = 3.25 > t 0.05 = 1.75) concentrations in the water and soil was determined in the lowest parts of the relief (<0 m), when the floodwater was at more than 1 km distance from the riverbed. The concentrations of the tested ions at the beginning of flood reflect the amount of substances carried from the catchment areas into the rivers. The quality of the water flowing through the valley depended on the relief height, flow velocities and distribution and soil properties.