A major step in developing legislatively mandated ecological flows for watercourses in Florida, USA is the selection of an appropriate baseline flow period. Recently climatologists have established a link between multidecadal periods of warming and cooling of the Atlantic Ocean (the Atlantic Multidecadal Oscillation (AMO)) and rainfall patterns across much of North America. During an AMO warm period (pre-1970), much of North America received less than average rainfall, while during a multidecadal cool period (post-1970), much of North America experienced above normal rainfall. There are exceptions to this general trend with some areas of North America showing an opposite relationship with the AMO. Peninsular Florida is one of these exceptions. While analysing flows on a number of rivers in south–central Florida, we observed a step rather than a monotonic trend in flows consistent with a switch from a warm multidecadal period to a cool multidecadal period. We examined river flows at all gaging sites throughout Florida and the southeast United States that had flow records of 60 years or more. Three river flow patterns were clearly discerned: a Southern River Flow Pattern (SRP) where flows are seasonally greatest during the summer months (June–September); a Northern River Flow Pattern (NRP) where flows are seasonally greatest in the spring and a Bimodal River Flow Pattern (BRP) with distinct peaks in rainfall and flow both in spring and summer. Those rivers with a BRP occur in a band that stretches diagonally from the northeast corner of Florida (St. Marys River) and runs in a southwest direction to the big bend area of the state near the mouth of the Suwannee River. Rivers to the north of this line exhibit the NRP, while rivers to the south of this line exhibit the SRP. Rivers with the SRP exhibited consistently lower flows during the AMO cool period and consistently higher flows during the AMO warm period. Differences in flow volumes between multidecadal periods averaged 30% in SRP rivers. Rivers with a NRP showed an opposite trend. Most convincingly, rivers with the BRP exhibited both trends, the spring mode responded similarly to the northern rivers while the summer mode followed the southern river trend. These results have important implications not only for the establishment of ecological flows, but also for water supply planning and development, flood control and stream ecology in general, since there are considerable differences in the magnitude of flows that should naturally be expected between multidecadal periods. Relatively large decreases and increases in flow are attributable to rainfall differences between multidecadal periods. Copyright © 2008 John Wiley & Sons, Ltd.