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 <0.06 mg/L, resulting from anoxic conditions and elevated DOC concentrations that favored denitrification. Although most parts of the partially confined UFA in the SANT study area were anoxic or had mixed redox conditions, water from 28 % of the sampled wells was oxic and had low DOC concentrations. Based on the groundwater age information, nitrate concentrations reflect historic fertilizer N usage in both the study areas, but with a lag time of about 15–20 years. Simulated responses to future management scenarios of fertilizer N inputs indicated that elevated nitrate-N concentrations would likely persist in oxic parts of the surficial aquifer and UFA for decades even with substantial decreases in fertilizer N inputs over the next 40 years.