Five years of monthly data of indicator bacteria from 1998 to 2002 were evaluated to find out the changes in water quality during the rehabilitation of the Golden Horn, an estuary severely polluted from industrial and domestic discharges since the 1950s. Surface fecal coliform was above 106 CFU/100 ml at the inner part in 1998. Following the achievement of healthy water circulation and control of most surface discharges, fecal coliform and fecal streptococci counts decreased below 103 CFU/100 ml in the summer of 2002. However, the decrease was interrupted by sudden shifts in rainy periods. Runoff, enhanced by domestic inputs during rainfall, has become the main factor influencing water quality in the estuary today. Increasing values of fecal coliform were observed during periods of low salinity, pH, dissolved oxygen and high ortho-phosphate, whilst decreasing values were detected during high salinity, pH and dissolved oxygen and low ortho-phosphate periods. Striking changes were observed within five years, promising that even an anoxic water body can turn into a recreational area with appropriate treatment.