Phytoplankton communities play a significant role in the oceanic biological pump by forming
the base of the trophic structure. Increase in nutrients loading affects spatial and temporal distribution of phytoplankton. This study examined the phytoplankton community structure and ecological indices in relation to nutrients dynamics in both estuarine and oceanic areas of Ramisi-Vanga systems along the Kenyan coast. Surface water samples were collected and analysed for nutrients (PO4 3--P, NO3 --N and NH4 +-N) and phytoplankton abundance and community structure. This study reported very diverse phytoplankton community structure consisting of 88 taxa that were dominated by Chaetoceros sp., Coscinodiscus sp., Nitzschia sp., Pseudo-nitzschia sp., Alexandrium sp., Protoperidium sp. and Prorocentrum sp that are among
the potentially harmful algae. Diatoms were the most abundant taxa in Ramisi-Vanga system. Phytoplankton abundance was found to be higher in the estuarine systems (1182.06±149.14 cells/L) as compared to the oceanic systems (551.99±166.70 cells/L) with high abundance observed in May for oceanic and estuarine systems. Shannon Weiner’s species diversity index was greater than 2 in both oceanic and estuarine systems. Phytoplankton species’ abundance, composition and diversity were found to be influenced by the availability
of NH4 +-N, NO3 --N and PO4 3--P. Phytoplankton cell density was below 4000 cells/ L, thus, this study has classified Ramisi-Vanga system as an oligotrophic system implying that the current level of land based activities are not having significant impacts on the phytoplankton communities.