Much progress has been made in recent years towards a set of recognition criteria for river discharge variability in river channel deposits, and thus sedimentary proxies for precipitation variability. Despite this progress, there is currently no consensus on how different styles of discharge variability are reflected in river sedimentary records, and whether variable-discharge river records from different climate types can be distinguished. Herein, river discharge and precipitation variability in the Paleogene is investigated using associations between river channel and floodplain deposits across the Paleocene-Eocene boundary from the Paleocene upper Nacimiento Formation and the early Eocene San Jose Formation in the San Juan Basin, New Mexico, USA. The succession is identified as deposits of variable-discharge river systems based on shared channel-deposit characteristics with modern and ancient variable-discharge river systems and the proposed facies models, in addition to alternations of poorly drained and well-drained floodplain deposits and/or slickensides indicating alternating wet-dry cycles. A long-term stratigraphic trend toward increasingly well-drained floodplain deposits is also observed and hypothesized to indicate successively more arid conditions from the Paleocene into the early Eocene. Comparisons with modern rivers from various climate zones suggest a long-term shift from a monsoonal climate in the Paleocene, to a fluctuating subhumid climate, ultimately leading to semiarid to arid conditions in the early Eocene. These observations suggest that floodplain deposits may be a better indicator of ambient climate, whereas channel deposits are records for frequency and magnitude of high-intensity precipitation events. Therefore, the existing facies models for variable-discharge rivers that consider only channel facies may not capture critical information needed to make accurate interpretations of paleoclimatic conditions. This study also adds to a growing body of evidence from geologic records of mid-latitude Paleogene river systems suggesting increases in the magnitude or variability of river discharge coinciding with established climate perturbations.