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