In this study, we are aiming to test suitability of S2 MSI data for mapping water quality over four morphologically and optically different water bodies, as discovered from in situ measured remote sensing reflectance, in Lithuania: Plateliai and Dusia lakes – categorized as oligo-mesotrophic water bodies; Kaunas reservoir and the Curonian Lagoon – categorized as eutrophic water bodies with massive growth of harmful cyanobacteria blooms. We demonstrate Earth Observation (EO) as a valuable tool for i) water quality assessment according WFD, ii) cyanobacteria scum and anoxia risk mapping and iii) bathing conditions. Research was Co-funded by the Government of Lithuania through an ESA Contract under the PECS (Plan for European Cooperating States), TODAY project.