Quantitative paleoecological reconstructions using biological proxies, such as diatoms, Cladocera, and chironomids, have revolutionized paleolimnology and have greatly contributed to the understanding of the past local and regional environmental changes, as well as to nature conservation. While macrophytes are good ecological indicators, they have rarely been used to reconstruct past lake-water chemistry. The present study investigates which environmental variable best explains aquatic plant community composition in Finnish, Polish, and Swedish lakes for its further use in quantitative paleoenvironmental reconstructions. The method involved the creation of a modern macrophyte-environment calibration dataset, calculation of modern calibration functions using simple averaging regression, and final reconstruction of past environmental conditions in Lake Linówek (NE Poland) from a fossil assemblage using weighted averaging calibration. The data demonstrate that conductivity and alkalinity best explained macrophyte community composition in our dataset. Species “optima” for alkalinity were influenced by the presence/absence of carbon concentrating mechanisms (CCMs), enabling the utilization of HCO3− as a carbon source. Quantitative paleoenvironmental reconstruction indicates that past water conductivity and alkalinity fluctuated depending on internal lake processes and the supply of basic ions to the lake from the catchment related to climate and soil development in the watershed during the late Glacial (∼14,500–11,700 calibrated years before the present; cal BP) and the Holocene (11,700 cal BP–recent). We conclude that macrophytes can be successfully used for past lake-water chemistry reconstruction. Furthermore, calculated modern calibration functions for conductivity and alkalinity can be used in nature conservation for determining habitat requirements of numerous endangered macrophyte species as a basis for successful (re)introductions.