Abstract Studies of the phytoplankton community were conducted in the north-western Arabian Gulf in 2005 and 2006. Seven stations throughout Kuwait’s waters were sampled. The influence of nutrient-rich freshwaters from the Shatt al-Arab resulted in high phytoplankton productivity characterized by high species diversity with a strong dominance of diatoms, especially in northern Kuwait. Phytoplankton species richness gradually increased from north to south. Spatial distribution of both total abundance and biomass of phytoplankton indicated significant differences in species structure and size spectrum of the microalgae. The analysis of the temporal and spatial phytoplankton variability (distribution of total abundance and biomass, similarity of species compositions and local community structure) indicated that Kuwait’s northern waters differed from areas further south in terms of phytoplankton structure and temporal and spatial variability. Environmental heterogeneity is mainly attributed to the influence of the Shatt al-Arab system, which affects the temporal and spatial variability of the phytoplankton community.