Rapid population growth, urban sprawl, and increased agricultural production in the Apalachicola-Chattahoochee-Flint (ACF) river basin are threatening the availability of freshwater resources and greatly affecting the supply of freshwater to Apalachicola Bay, which supports a struggling shellfish industry. As a result, Alabama, Georgia, and Florida have been fighting over the allocation of ACF river basin water for the past three decades. The water conflict heats up every time there is drought in the basin. In the Southeast U.S., droughts are mainly caused by the La Niña phase of the seasonal-to-interannual climate variability phenomenon known as the El Niño Southern Oscillation (ENSO). Understanding and quantifying the impact of ENSO-induced climate variability on precipitation, soil moisture, streamflows, and groundwater levels can provide valuable information for sustainable management of water resources in this region. This study was undertaken to quantify the impact of ENSO on groundwater levels in the lower ACF river basin, an area highly dependent on groundwater for agricultural water use. Twenty-one observation wells with 30 years of monthly groundwater level data were used to study the ENSO-groundwater level relationship. Wavelet analysis techniques were used to study the teleconnection between ENSO and groundwater levels, while Mann-Whitney tests were conducted to quantify the impact. The effect of prolonged La Niña events on groundwater levels and their corresponding recovery periods were also studied. Results indicate a strong relationship between groundwater level fluctuations and ENSO. This relationship was found to be stronger during the recharge season (December-April) as compared to the non-recharge or agricultural irrigation season (May-November). The results obtained can be used to develop procedures for forecasting groundwater levels, which can then be used to better manage the groundwater resources of this region. © 2014 American Society of Agricultural and Biological Engineers.