This paper focuses on high-resolution analysis of pollen and sedimentology and botanical macro-remains analysis in a core from Lake Banyoles (Girona, Spain). The core sequence comprises a high resolution mid-Holocene (ca. 8.9–3.35 cal ka BP) vegetation succession, and sedimentological, geochemical and geomorphological proxies are related to both climatic and anthropogenic causes. Deforestation processes affected natural vegetation development in the Early Neolithic (7.25–5.55 cal ka BP) and Late Neolithic (5.17–3.71 cal ka BP), in the context of broadleaf deciduous forest resilience against cooling and drying oscillations. Changes in sedimentation dynamics and in lake water level caused the emergence of dry land on the lake margin where riparian forest was established from 5.55 cal ka BP onwards. The data show that in the context of an increasing aridification process, Neolithic land-use played an important role in vegetation history and environmental evolution.