To better understand the impact of channel migration processes and climate change on the depositional dynamics of floodplain lakes of the upper Amazon Basin during the late Holocene, we collected three sediment cores from floodplain lakes of the Ucayali River and one from the Marañón River. The cores were dated with 14C, radiographed and described. Bulk density, grain size analysis and total organic carbon (TOC) were determined. The results show that sedimentation in Ucayali floodplain lakes was marked by variations during the late Holocene, with periods of intense hydrodynamic energy and abrupt accumulations, a gap in the record between about 2870 and 690 cal yr BP, and periods of more lacustrine conditions. These changes in sedimentation were associated with variations in the river's influence related to changes in its meandering course (2870 cal yr BP) and a period of severe flooding between 3550 and 3000 cal yr BP. Lake Lagarto on the Marañón River floodplain exhibits a different sedimentary environment of low hydrodynamics with palm trees and macrophytes. Apparently, the lake has not experienced intense migration processes during the last 600 cal yr BP (base of the core). Nevertheless, the river sediment flux to the lake was important from 600 to 500 cal yr BP, although it decreased thereafter until the present. This decrease in the mineral accumulation rate indicates a decrease in river discharge since 500 cal yr BP, which coincides with precipitation records from the central Andes. In the upper part of the three Ucayali floodplain cores, a 30- to 250-cm-thick layer of reworked sediments has been deposited since 1950 AD (post-bomb). In Lake Carmen, this layer is associated with invasion of the lake by the levee of a migrating meander of the Ucayali. In Lakes Hubos and La Moringa, however, the river is still far away and the deposition must be interpreted as the result of extreme flooding. The beginning of the Ucayali meander migration is dated back to 2000 AD, suggesting that these extreme floods could be very recent and linked to hydrologic extremes registered instrumentally in the Amazon Basin.