Both phytoplankton of the Kizilirmak River/Black Sea transition zone and their interactions with nutrients were investigated between July 2007 and December 2008. A total of 447 taxa belonging to the divisions: Cyanobacteria (24), Bacillariophyta (209), Bigyra (1), Cercozoa (1), Charophyta (11), Chlorophyta (32), Cryptophyta (11), Miozoa (119), Euglenozoa (14), Haptophyta (13), Ochrophyta (10) and Protozoa Incertae Sedis (2) were identified at 5 different sites in the study area. Seventy four taxa were recognized as new records for the Algal Flora of Turkey and 41 taxa were determined as HAB (Harmful Algal Bloom) organisms. According to the hierarchical clustering and MDS analyses, surface phytoplankton were distributed along the salinity gradient from freshwater to saline waters, and the early spring samples were separated from the other samples. However, in addition to the agglomerative hierarchical cluster analysis, the samples were divided into four groups - "Fresh", "Brackish", "Marine" and "Early spring-Marine" - as a result of MDS analysis. The results of this study revealed that the surface phytoplankton were influenced by the salinity and the Secchi Disc depth together with the seasonal water temperature dynamics and NO3-N concentrations throughout the research period.