Two stages of high-discharge fluvial deposition during the last phase of the Late Holocene are recorded in the infilling of a palaeochannel in the distal reach of the Pecora river, a small catchment along the Tyrrhenian coast of Tuscany (Central Italy). Facies analysis shows an abrupt change from high sinuosity gravelly-sandy river (III-I millennium BC) to shallow braided channel bars (VII-XII century AD). The second stage features the occurrence of very abundant sediments originated from the erosion of the upstream Calcareous Tufa environments, coupled with abundant fine- to coarse-sized charcoal fragments, derived by selective fires sequentially affecting the wetlands, the riparian vegetation, and the surrounding slopes. Geomorphological and stratigraphical analysis of the Pecora river catchment indicates that the widespread wetlands in which Calcareous Tufa were developing were already active around 4 ka cal BC and their formation ended permanently around the XIII century AD. The age of the decline of the tufa systems in the Pecora catchment seems to disagree with most of those recorded in Europe. Contrastingly, their inactivity is coeval with the occupational period of the medieval archaeological site of Vetricella, located in the surroundings of the palaeochannel, and the onset of upstream wetland reclamation and hydraulic works. These changes led to the reclamation of karst depressions, the capture of karst springs, the bypass of barrages and the deep downcutting of the tufa terraces and the drainage of the corresponding wet environments. This study discusses the anthropogenic factors that during the Early Middle Age affected the Pecora catchment and promoted a permanent change in its physical and biological environment with a new assessment of the river course and the reclamation of large portions of floodplains previously permanently flooded. This study provides new data regarding the decline of fluvial tufa in the Mediterranean area and emphasises the Early Medieval anthropogenic forcing mechanism tethered to agricultural practices and land management, contrasting with the classic historical model which suggests an almost complete abandonment of the alluvial and coastal plains.