The variation in phytoplankton community as a response to improving water quality has been studied in the severely polluted Golden Horn Estuary (GHE). Phytoplankton data collected monthly for 4 years and a detailed set of environmental parameters clearly showed the remarkable change in the GHE. The GHE ecosystem did not respond to numerous rehabilitation efforts to improve water quality, unless strict measures were taken to enhance water circulation. The opening of a bridge operating on large buoys and release of high amounts of fresh water from a dam acted as the turning point for the whole system. The weakening of light limitation and anoxia at upper regions is followed by consecutive blooms of different species/groups and resulted in super-saturated dissolved oxygen concentrations and a significant decrease in nutrient concentrations. When compared to the pre-remediation period, average total eukaryotic phytoplankton abundance increased 11-fold in the lower estuary, while the increase in the upper estuary was over 3 x 10(4) in the post-remediation period. In addition, species richness continuously increased through the study period and community structure showed very strong variability. Since the estuarine ecosystem is controlled by precipitation in the last decade, the increase in anthropogenic/terrestrial inputs following heavy rainfall had adversely affected water quality and phytoplankton.