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Chlorophyll a (Chl a) and phaeopigments a (Phaeo a) spatial distribution in the Western Black Sea was studied in relation to environmental factors and mesozooplankton community. For that purpose, CTD parameters, nutrients, chlorophyll pigments, and mesozooplankton total density and biomass were measured at 33 stations, distributed along the Romanian shelf waters, in June 2016. The studied area was divided into 4 subareas (NIS – northern inner shelf, NOS – northern outer shelf, SIS – southern inner shelf, and SOS – southern outer shelf). The hydrological regime, characterized by large Danube’s flow and a coastal upwelling phenomenon observed both in the NIS and SIS, strongly influenced the spatial variability of Chl a and Phaeo a. Surface Chl a and Phaeo a showed the highest concentrations within NIS, followed by NOS, both subareas subjected to larger freshwater input from the Danube River. The vertical distribution of Chl a in the inner shelf waters generally showed a subsurface maximum layer within 6–24 m (the shallower and stronger ones within NIS). The outer shelf waters displayed two subsurface maxima; an upper one (within 7–20 m) and a deeper one, slightly higher than the upper one, observed both in NOS and SOS at 30–45 m depth. Phaeo a showed relatively similar vertical profiles to Chl a, with a subsurface maximum generally coinciding with subsurface chlorophyll maximum. The meroplankton showed positive correlations with the chlorophyll pigments, which suggest a strong link between pigments abundances and distribution and development and production of larvae in the coastal waters.