A twelve year (2000 2011) study of three coastal lagoons in the Gulf of Mexico was conducted to assess the impacts of local watershed development and tropical storms on water quality. The lagoons have similar physical and hydrological characteristics, but differ substantially in the degree of watershed urban development and nutrient loading rates. In total the lagoons experienced 22 storm events during the period studied. Specifically, we examine (1) whether there are influences on water quality in the lagoons from watershed development, (2) whether there are influences on water quality in the lagoons from storm activity, and (3) whether water quality is affected to a greater degree by watershed development versus storm activity. The two urbanized lagoons typically showed higher water-column nitrate, dissolved organic nitrogen, and phosphate compared with the non-urbanized lagoon. One of the urbanized lagoons had higher water-column chlorophyll a concentrations than the other two lagoons on most sampling dates, and higher light extinction coefficients on some sampling dates. The non-urbanized lagoon had higher water-column dissolved oxygen concentrations than other lagoons on many sampling dates. Our results suggest long-term influences of watershed development on coastal water quality. We also found some evidence of significant storm effects on water quality, such as increased nitrate, phosphate, and dissolved oxygen, and decreased salinity and water temperature. However, the influences of watershed development on water quality were greater. These results suggest that changes in water quality induced by human watershed development pervade despite the storm effects. These findings may be useful for environmental management since they suggest that storms do not profoundly alter long-term changes in water quality that resulted from human development of watersheds.