Summary The Mediterranean seagrass Posidonia oceanica maintains a biodiverse ecosystem and it is a world‐wide important carbon sink. It grows for millennia, accumulating organic‐rich soils (mats) beneath the meadows. This marine habitat is protected by the European Union; however, it is declining rapidly due to coastal development. Understanding its response to disturbances could inform habitat restoration, but many environmental impacts predate monitoring programs (<50 years). This research explores the palaeoecological potential of Posidonia mats to reconstruct six thousand years of environmental change that could have affected Posidonia meadows and, in turn, left an imprint on the mats. Palynological, microcharcoal, magnetic susceptibility and glomalin‐related soil protein (GRSP) analyses on Posidonia mats enabled us to detect climate‐ and human‐induced environmental processes impacting on the seagrass during the Late Holocene. The pollen and microcharcoal records reconstructed anthropogenic disturbances attributed to agriculture. The record of GRSP shows that agrarian activities affected continental soil quality. Changes in magnetic susceptibility reveal that enhanced soil erosion was caused by both climate (major flooding events in the NW Mediterranean) and humans (cultivation) which impacted on the Posidonia mat. Finally, increased human impact is linked to eutrophication of coastal waters since Roman‐Medieval times. Synthesis. This study shows that climate and land‐use changes in the western Mediterranean resulted in enhanced loadings of terrigenous material to the coastal zone since the Late Holocene, likely disturbing the Posidonia meadows and their mat carbon accumulation dynamics. Under the current global change scenario in which CO2 emissions are projected to increase, restoring carbon sinks is a priority. Seagrass habitat restoration should consider not only the coastal perturbations, but also the continental ones at a catchment scale to preserve the socio‐economic ecosystem services provided by seagrasses.