Phytoplankton pigment composition and associated biochemical (chlorophyll a, nitrate+nitrite, ammonia, phosphate, silicate) and physical (temperature, salinity) parameters were studied seasonally in the river-fed eutrophic coastal and oligotrophic offshore waters of the Mersin Bay located on NE Mediterranean. Total chlorophyll a concentrations varied seasonally between 0.023 - 7.73 µg/l in the river fed coastal zone (salinity: 36.54-39.68), exhibiting less seasonality in the offshore station (0.01 – 0.91 µg/l). Seven different phytoplankton taxa (namely diatoms, cyanobacteria, prymnesiophytes, dinoflagellates, chlorophytes, chrysophytes, prochlorophytes), determined by High Performance Liquid Chromatography (HPLC), were consistently present in the coastal waters during 2008-2011. The predominant diatom and coccolithophorid taxa in the river-fed coastal waters were replaced by prokaryotic picoplankters (cyanobacteria & prochlorophytes) and prymnesiophytes in the offshore. Contribution of prokaryotic picoplankton and eukaryotic nanoflagellates to total chlorophyll (% 23 to 47 and % 28 to 43, respectively) increased by about 50% from the coastal to the offshore station. Contribution of large cells to total chlorophyll decreased from 49% to 10% towards offshore. Prochlorophytes were observed as the dominant group in relatively colder and darker deep waters.