The Water Framework Directive (WFD) provides the basis for developing a system to protect and restore the aquatic environment. Macrophytes are one of the groups of organisms for determining ecological status of lakes. Using partial least squares regression (PLS-R), we showed relationships between conductivity and chlorophyll a (to a lesser extent nutrient concentrations) and Ecological State Macrophyte Index (ESMI) values. However, catchment land use/cover (LU/LC) appears to be the important factor affecting macrophyte diversity as expressed by ESMI. The presence of significant correlations was found for the catchment area determined from surface runoff using the platform SCALGO Live, based on a permanently updated numerical terrain model and an accurate land use/cover database used in Poland BDOT10k. The Corine Land Cover (CLC) database commonly used in the EU appeared to be of insufficient resolution. We have shown a high positive impact of the presence of wetlands and reservoirs in the catchment on ESMI values and negative for agricultural and urbanized areas. Obtaining information on lake catchment land use and land cover is costless. Relating LU/LC to lake macrophyte assessment methods allows this no-cost method to be included in the set of biological methods for assessing lake condition. Understanding the factors that determine the condition of lakes is fundamental to managing them according to the requirements of the WFD. The results of our study indicate that the integration of lake catchment area planning with lake water management is imperative.