The present paper aims to reconstruct the Lower Tagus Valley flooding history for the last ca. 6500 a, to explore the suitability of pollen-based local vegetation development in supporting the reconstruction of flooding history, and to explain fluvial activity changes in terms of allogenic (climate, human impact) and autogenic (system intrinsic) processes. The flooding history has been determined by cored sedimentary records located ∼18 km apart in distal, low-energy backswamps on both sides of the Tagus channel. In these low-energy backswamps, fine-grained sediment layers deposited from suspended load of overbank flood water reflect periods with multiple overbank floods. By means of a multi-proxy approach (sedimentology, magnetic susceptibility, grain size, loss-on-ignition, carbonate content and pollen), sedimentary and environmental changes were identified. At both sites, synchronous lithological intervals accumulated, suggesting a common origin for the changes in fluvial activity since ca. 6500 cal. a BP. Based on lithological changes, three phases of high fluvial activity (6500–5500, 4900–3500 and 1000–0 cal. a BP) and two phases of low fluvial activity (5500–4900 and 3500–1000 cal. a BP) were identified. Two periods with dominant allogenic controls on fluvial activity in the Lower Tagus Valley were identified: relative sea level (6500–5500 cal. a BP) and human impact (1000–0 cal. a BP). During the intermediate period, changes in fluvial activity may have been caused by climate (5500–1000 cal. BP), but unambiguous correlations are difficult to make. This is due to the way allogenic controls are translated through the fluvial system, the geomorphological differences between upstream and downstream studies and autogenic processes. The comparison of local vegetation development and flooding phases as reconstructed using sedimentology shows a limited added value of using local palynology as a proxy for fluvial activity. Copyright © 2010 John Wiley & Sons, Ltd.