Differences in the degree of confinement, redox conditions, and dissolved organic carbon (DOC) are the main factors that control the persistence of nitrate and pesticides in the Upper Floridan aquifer (UFA) and overlying surficial aquifer beneath two agricultural areas in the southeastern US. Groundwater samples were collected multiple times from 66 wells during 1993–2007 in a study area in southwestern Georgia (ACFB) and from 48 wells in 1997–98 and 2007–08 in a study area in South Carolina (SANT) as part of the US Geological Survey National Water-Quality Assessment Program. In the ACFB study area, where karst features are prevalent, elevated nitrate-N concentrations in the oxic unconfined UFA (median 2.5 mg/L) were significantly (p = 0.03) higher than those in the overlying oxic surficial aquifer (median 1.5 mg/L). Concentrations of atrazine and deethylatrazine (DEA; the most frequently detected pesticide and degradate) were higher in more recent groundwater samples from the ACFB study area than in samples collected prior to 2000. Conversely, in the SANT study area, nitrate-N concentrations in the UFA were mostly