Our aim was to test the hypothesis that precipitation of calcite encrustation and accumulation of phosphorus by charophytes depend on both habitat conditions and plant species. To do this, we analysed the amount of calcite and phosphorus fractions in six charophyte species from ten lakes of different water chemistry. Percent of calcite encrustation in plant biomass was species specific—Chara rudis and Chara tomentosa produced most and Chara globularis and Chara intermedia least calcite. Lake water supersaturation with calcium carbonate was not necessary to induce calcite formation. Calcium and soluble phosphorus in lake water exerted significant (positive and negative, respectively) effect on calcite variability across species. Soluble and total phosphorus in lake water, however, were poor predictors of total phosphorus variability in plants. All plants accumulated more inorganic than organic phosphorus. Concentration of calcium-bound phosphorus per gram of calcite showed significant interspecific differences. Our data suggest that charophytes are capable of accumulating relatively large amounts of calcium carbonate and phosphorus (mostly calcium-bound P) in lake sediments.