The abundance pattern and species diversity of phytoplankton in the surface waters of the Golden Horn Estuary were investigated between August 2011 and July 2012 in relation to environmental factors. Seventy-eight phytoplankton taxa (38 diatoms, 30 dinoflagellates and 10 phytoflagellates) belonging to eight taxonomic classes were identified in bottle and net samples. Phytoplankton abundance increased in spring and summer (from March to August) and reached its highest (10,429 x 10(3) cells L-1) during the bloom of Heterosigma akashiwo (Raphidophyceae) in the middle and upper estuary in late May. In general, phytoplankton abundance was higher in the middle estuary indicating more suitable conditions for phytoplankton growth, while species richness and diversity was higher in the lower estuary. The most abundant species were Skeletonema marinoi and Thalassiosira sp. among diatoms; Scrippsiella trochoidea among dinoflagellates; Plagioselmis prolonga and Heterosigma akashiwo among phytoflagellates. Diatoms were more abundant in the lower and middle estuary, while dinoflagellates and phytoflagellates in the upper estuary. The main factors causing the spatio-temporal variation of phytoplankton in the study area were temperature, salinity, water transparency and nutrients. Water transparency in the upper estuary is mostly influenced by organic and inorganic matter carried by two streams. As a result, this area should be considered a potential risk area for future algal blooms.