The Pantanal is the world's largest tropical wetland and a biodiversity hotspot, yet its response to Quaternary environmental change is unclear. To address this problem, sediment cores from shallow lakes connected to the UpperParaguayRiver (PR) were analyzed and radiocarbon dated to track changes in sedimentary environments. Stratal relations, detrital particle size, multiple biogeochemical indicators, and sponge spicules suggest fluctuating lake-level lowstand conditions between ~ 11,000 and 5300 cal yr BP, punctuated by sporadic and in some cases erosive flood flows. A hiatus has been recorded from ~ 5300 to 2600 cal yr BP, spurred by confinement of the PR within its channel during an episode of profound regional drought. Sustained PR flooding caused a transgression after ~ 2600 cal yr BP, with lake-level highstand conditions appearing during the Little Ice Age. Holocene PR floodpulsedynamics are best explained by variability in effective precipitation, likely driven by insolation and tropical sea-surface temperature gradients. Our results provide novel support for hypotheses on: (1) stratigraphic discontinuity of floodplain sedimentary archives; (2) late Holocene methane flux from Southern Hemisphere wetlands; and (3) pre-colonial indigenous ceramics traditions in western Brazil.