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Empirical Orthogonal Function (EOF), wavelet, and wavelet coherence analysis of baseflow time-series from 126 streamgauges (record-length > 50 years; small and mid-size watersheds) in the US South Atlantic (USSA) region reveal three principal modes of space-time variability: (1) a region-wide dominant mode tied to annual precipitation that exhibits non-stationary decadal variability after the mid 1990s concurrent with the warming of the AMO (Atlantic Multidecadal Oscillation); (2) two spatial modes, east and west of the Blue Ridge, exhibiting nonstationary seasonal to sub-decadal variability before and after 1990 attributed to complex nonlinear interactions between ENSO and AMO impacting precipitation and recharge; and (3) deep (decadal) and shallow (< 6 years) space-time modes of groundwater variability separating basins with high and low annual mean baseflow fraction (MBF) by physiographic region. The results explain the propagation of multiscale climate variability into the regional groundwater system through recharge modulated by topography, geomorphology, and geology to determine the spatial organization of baseflow variability at decadal (and longer) time-scales, that is, deep hydrologic drought. Further, these findings suggest potential for long-range predictability of hydrological drought in small and mid-size watersheds, where baseflow is a robust indicator of nonstationary yield capacity of the underlying groundwater basins. Predictive associations between climate mode indices and deep baseflow (e.g. persistent decreases of the decadal-scale components of baseflow during the cold phase of the AMO in the USSA) can be instrumental toward improving forecast lead-times and long-range mitigation of severe drought.