Tropical wetlands such as the Pantanal help regulate global biogeochemical cycles, but climate change is modifying these environments. Controls on environmental changes can potentially be assessed from ancient, well-dated lacustrine sedimentary records. An integrated field and laboratory approach was undertaken to study the limnogeology of Lake Uberaba in the northern Pantanal, and test whether the lake has preserved a reliable record of environmental change in its strata. This study was designed to understand how the basin accumulates sediment and to assess its sensitivity to hydroclimatic variability. The data showed that modern Lake Uberaba is a highly dynamic, freshwater fluvial-lacustrine basin. Modern lake floor sediments are largely siliciclastic silts, with limited organic matter content and abundant sponge spicules. This sedimentary composition reflects the lake’s open hydrology and well-mixed water column. Limited data from sediment cores indicates that Lake Uberaba may have formed ~1760 CE, following an abrupt transgression over an oxidized floodplain depositional environment. The stratal contact between lacustrine and floodplain deposits suggests the presence of an erosional unconformity, the timing and duration of which remains unknown. The environmental change favoring lake formation appears to be linked to increased effective precipitation provided by the Intertropical Convergence Zone (ITCZ) in the northern Pantanal.