One of the main purposes of the lake is flood control downstream of the lake, mainly protecting metro Atlanta. There have only been two major flooding events on the downstream section since the construction of Buford Dam. The most recent flooding event was in 2004, after the remnants of two major hurricanes(Hurricane Frances and Hurricane Ivan) dropped huge amounts of rainfall across the area.

In July 2009, a federal judge from Minnesota (chosen as an arbiter from a neutral location) ruled that Congress never authorized Lake Lanier to be used as a source of the water supply for metro Atlanta. Alabama and Florida contend that Lake Lanier was created for three primary purposes: hydropower generation, river navigation and flood control. The state was given three years to stop withdrawing from the lake (except for the adjacent cities of Gainesville and Buford), unless Congress authorizes it, or the three states which use the basin come to an agreement. The Atlanta Regional Commission chairman noted that if enforced, cutting drinking water to 75% of the region would requiredisaster aid from FEMA.

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