The Maximum Chlorophyll Index (MCI), developed for the MERIS sensor processing scheme, is used to investigate the seasonaldynamics, spatial distribution, and coverage of cyanobacterial blooms over Lake Peipsi (Estonia/Russia) and Lake Võrtsjärv(Estonia). In these optically complex waters, the amounts of suspended matter and dissolved organic matter vary greatly andindependently of the phytoplankton biomass. We demonstrate that MCI is a useful, new tool for detecting and estimating cyanobacterialbiomass (R2 = 0.73), phytoplankton biomass (R2 = 0.70) and chlorophyll a concentration (R2 = 0.64). The MCI-derivedresults are consistent with known patterns of phytoplankton dynamics in these lakes, whose optical properties are in the same range as in many coastalregions of the Baltic Sea
