Freshwater input helps to determine estuarine characteristics and may be influenced by climate oscillations. We examined monthly variability in river discharge to the Ogeechee, Altamaha, Satilla, and St. Marys River estuaries (GA, USA) in relation to three climate indices: the Bermuda High Index (BHI), the Southern Oscillation Index (SOI), and the Atlantic Multidecadal Oscillation (AMO). Regionally consistent, seasonally alternating patterns emerged: BHI was correlated with river discharge from late spring through fall; SOI was correlated with river discharge in the winter and early spring; and AMO correlations with river discharge were less consistent but were strongest in winter. Climate variations during recent drought and flood events appear to bear out the overall correlation patterns that we found over longer historical periods. The seasonal change in dominance of different climate signals could lead to differential climate signal propagation throughout an ecosystem, depending on critical seasons for growth, reproduction, or other ecosystem processes. Understanding how climate patterns affect freshwater input will help elucidate how these estuarine ecosystems may respond to climate changes.