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While chlorophyll a fluorescence is well documented and widely used to study phytoplankton biomass and its photosynthetic activity, the spectral properties of bacteriochlorophylls (BChls) are still poorly described. Green sulfur bacteria (Chlorobiaceae) represent obligately anaerobic photoautotrophic bacteria with anoxygenic type of photosynthesis. Two types of green sulfur bacteria differ in pigments: green-colored strains contain BChl c, d and carotenoid chlorobactin; brown colored ones contain BChl e and carotenoid isorenieratin. In addition BChl a and chlorophyll a are also present. Fluorescence of green sulfur bacteria excited with the blue light demonstrates two overlapping bands: the emission of so called chlorosome chlorophylls (BChls c, d and e) in the range 740-770 nm and the emission of BChl a with maximum at 815 nm. The intensity of BChls fluorescence reflects total concentration of pigments in the cells and can be used to estimate biomass of phototrophic bacteria in water. We summarize the results of spectral measurements performed in 2015-2017 on water samples from several lagoons and lakes at the White Sea coast. In those stratified water reservoirs massive bacterial blooming can be found near the chemocline zone at depth about 2 m. From multiple studies it was discovered that depth distribution of BChl fluorescence intensity and BChl concentration estimated from extractions were not equivalent: water layer with maximal fluorescence typically was located 10-15 cm lower the layer with highest BChl concentration. This fact can be explained by BChl fluorescence quenching in upper layer of the chemocline with insufficient value of redox potential. The value of redox-dependent fluorescence quenching may serve as an indicator of physiological status of phototrophic bacteria of the transition zone and anaerobic layer.