The Noordoostpolder is an archaeologically rich area in the central Netherlands. A sediment profile, situated on a dune slope, was sampled near a Neolithic settlement site on the former island of Schokland. To reconstruct the local and regional vegetation around a Neolithic settlement, pollen, non-pollen palynomorphs and macrofossils were analyzed. The lowest part of the profile represents mid-Holocene peat growth on Pleistocene cover sand. Based on anthropogenic indicators like Cerealia and apophytes, the impact of early Neolithic people living in the nearby settlement was prominent. In addition to the pollen record, the spores of coprophilous fungi appeared to be valuable palaeoenvironmental indicators for human impact. The sampled sequence shows the effects of a rising water table related to sea level rise. The results support Cappers and Raemaekers’ (2008) model of small-scale wetland farming in the early Neolithic.