The Suwannee River watershed is extremely vulnerable to pollution because of its particular hydrological characteristics. The water interaction between surface water and groundwater exists to balance the river and the Upper Floridan aquifer via springs.

El Niño and La Niña events are responsible for the heavy precipitation in the watershed. Some El Niño events resulted in severe flood events, whereas some La Niña events resulted in drought events in the past several decades. Those extreme flood-drought events caused serious damages and losses of property and life in the watershed and constituted threats on the hydrological environments.

In El Niño years, groundwater can be endangered by the polluted flood water runoff, which drains development areas and phosphate deposit mines into sinkholes and springs. In La Niña years, the quality of river waters will be influenced by the groundwater with high nitrate concentrations. Coastal saltwater intrusion and insufficient nutrients near shore are possibly related to La Niña events. However, La Niña and drought events can help clean up the river itself. River sediments are hardened and compacted by sunlight and exposure to the atmosphere when the river drains dry. Pollutants are trapped in the river bottom or released to the atmosphere and excess nutrients are oxidized by the air.

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