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Photosynthetic organisms are an important object of optical researches in environmental monitoring. Photosynthetic organisms in aquatic environments modify the light penetrating the water column and reflection of solar radiation by absorption in pigmented structures and by light scattering. Fluorescent methods allow characterizing health, viability and ecological state of photosynthetic organisms. Field investigations of phytoplankton of Curonian Lagoon water were carried out. Curonian Lagoon, a reservoir separated from Baltic Sea by Curonian Spit, is important object of environmental monitoring. Agricultural territories and urban area of Kaliningrad region of Russia and Lithuania and national park Curonian Spit are located on the Curonian Lagoon shore. Cyanobacteria blooms is a great ecological problem of Curonian Lagoon and Baltic Sea. Cyanobacteria is a big group of photosynthetic organisms, which play great ecological role. In recent years cyanobacteria dominate in water ecosystems due to global climate change and anthropogenic eutrophication. Cyanobacteria blooms leads to toxin contaminations of water and severe disruptions in fisheries. These facts stimulate the researches in biophotonics of cyanobacteria into their natural habitat. Present study aims to development of optical methods to forecast cyanobacteria blooms. Investigations of optical properties of lagoon water, species composition of phytoplankton and functional state of cyanobacteria were conducted. Cyanobacteria concentration in water samples were determined by chlorophyll fluorescence method. Functional state and light adaptation parameters of cyanobacteria were measured using fluorescence induction and relaxation (FIRe) technique. Incident and reflected solar radiation were recorded using radiometer with visible and IR light spectra registration (these measurements were used to calibrate the data received from the satellite radiometers). Measuring was conducted in various area of Curonian Lagoon along the route of the boat. A weak cyanobacteria bloom with dominant specie Aphanizomenon flos-aquae was found in Curonian Lagoon at expedition time. Fluorescent characteristics and ecological state of cyanobacterial complex of lagoon under natural conditions were determined. Nonphotochemical quenching constants of wild type A. flos-aquae in natural conditions were measured. Concentration of photosynthetic organisms in various lagoon areas was fixed. Discovered, that the main characteristics of lagoon water during cyanobacteria bloom is ratio of two peaks in reflected light spectra, corresponding to phycocyanin and chlorophyll absorbance.