The impact of Hurricane Ivan on water quality in Pensacola Bay was investigated by MODIS 250m remote sensing of chlorophyll-a concentrations at different time slots before and after the hurricane event. Before the hurricane, the mean chlorophyll-a in the Bay was 5.3 μg/L. Heavy rainfall occurred during the hurricane landfall. The 48 h rainfall reached 40cm and the peak storm surge reached 3m on 9/16. After the rainstorm and during the storm surge on 9/17/2004, the mean chlorophyll-a concentration substantially increased to 14.7 μg/L. 26.3% water area was in the poor-water-quality condition (chl-a>20 μg/L). This indicates that heavy nutrient loads from urban stormwater runoff and storm-surge inundation simulated chlorophyll bloom. After the end of the storm surge on 9/18/2004, the mean chlorophyll dropped to 2.0 μg/L, suggesting the effective flushing of polluted water from the bay to the Gulf of Mexico by the storm-surge. The good water quality condition lasted for almost several weeks after the storm surge. The peak river flow, arriving on the 4th day after the peak storm surge, did not alter the good water quality situation in the bay. This indicates that urban stormwater runoff rather than the river inflow is the major pollutant source for water quality in Pensacola Bay during the hurricane.