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The vertical distribution of chlorophyll in coastal waters is influenced by a combination of the hydrodynamic environment and different biotic and abiotic processes. The spatial and temporal occurrences of chlorophyll profiles provide a good representation of the changes in the marine environment. The majority of studies in the Adriatic Sea have so far been conducted in areas unaffected by anthropogenic pressure. Our study site is located near two marine outfalls, which are part of the public sewage system. This study aims to characterize the chlorophyll vertical distribution and describe its variability based on the stratification conditions and the presence of a wastewater effluent plume. Based on these conditions, we identified three characteristic scenarios/types of chlorophyll profiles. The first one occurs when the vertical mixing of the water column creates the upwelling of chlorophyll and nutrients to the upper part of the water column. The second and third scenarios occur during stratified conditions and differ by the extent of the effluent plume intrusion. Using modern fluorescence techniques, we identified and described three different vertical chlorophyll profiles, characterizing them according to their physical and biological parameters and processes. For cases with a visible effluent intrusion, we confirmed the importance of the pycnocline formation in keeping the effluent below and maintaining the higher water quality status at the top of the water column. Full article