Along the shoreline of the White Sea, due to the post-glacial uplift of the coast, some water bodies with stable stratification have been formed. They have been classified as meromictic as they are at different stages of isolation from the Sea. As separation progresses, significant changes occur in the water column, including the composition of chromophoric dissolved organic matter (CDOM) and the structure of the aquatic microbial community. In this work, we searched for optical proxies of euxinia (anoxic conditions with accumulated hydrogen sulfide) in the water column of the meromictic lagoon on Zeleny Cape. The lagoon is separated from the White Sea basin by a shallow threshold that completely isolates the lagoon during low tide, but marine water enters the lagoon during high tide. The ecosystem in the lagoon is characterized by the marine salinity of water and a high organic matter content in the bottom water and sediments. In this study, spectral methods were used to obtain the depth distribution of CDOM, chlorophyll, and bacteriochlorophyll in the lagoon with strong water stratification and euxinic conditions in the bottom water. The measured optical CDOM characteristics were compared with hydrochemical data (water salinity, Eh, pH, dissolved oxygen), phytoplankton (oxygenic phototrophs), and green sulfur bacteria (anoxygenic phototrophs) distribution along the water column. The spectroscopic methods showed to have the advantages of not requiring water sample pre-treatment and allowing rapid sensing of CDOM and photosynthetic pigments at each horizon.