Incised valleys entirely filled with fluvial deposits are rarely described in the literature, and even rarer are accounts of incised valleys whose filling is not driven by relative sea-level changes. Valleys of this type have not been widely recognized in the stratigraphic record, because they are likely to occur in areas undergoing intense erosion or to be encased within alluvial deposits with no strong lithologic contrast. In this paper, an upper Pliocene fluvial valley fill, encased within shallow marine middle Pliocene deposits and pre-Neogene bedrock (eastern Siena Basin, Northern Apennines, Italy) and accumulated in response to tectonics and climate changes, is described. The recognition of this fluvial body (up to 40 m thick) in an incised-valley setting is based on its overall geometry, lithofacies characteristics, gravel composition, and fossil content. Upvalley fill is represented by amalgamated gravels emplaced by heavily sediment-laden flows, whereas downvalley fill shows a more organized depositional style and consists of two fining-upward successions. Notable is the presence at the top of the lower succession of decameter-thick floodplain fines, which extend from one valley wall to another and have no fine-grained correlatives in the upvalley fill. Valley incision resulted from a drop in relative sea level, arising from late middle Pliocene regional uplift. Stratigraphic and paleontological data constrain valley filling to the late Pliocene–early Pleistocene time span. Such a filling stemmed from an increase in sediment supply, which resulted from the interplay between uplift of the Chianti Ridge and a climatic change toward humid conditions, as recorded in the coeval strata of the adjacent Valdarno Basin. Beyond the regional significance, an important implication of the case study is that the incision and filling factors need not be genetically related. Moreover, the stratigraphic architecture of the studied fluvial fill is discussed in terms of the relations between sediment supply and sediment storage en route from the source area to the depositional site and their association with tectonic movements. Specifically, the valley-wide floodplain fines are thought to record the response of the fluvial system to a tectonic rejuvenation of catchments, which modified the valley gradient and promoted upstream gravel storage, whereas the overlying gravels manifest the reestablishment of a new equilibrium river profile.