This study presents the results of a palynological investigation on a sediment core from the seasonal and saline Lake Maharlou in the Zagros Mountains in southwest Iran. We emphasised studying the role of man in modifying the vegetation of the area and the dominant agricultural practices during the Imperial Persia period (2,500–1,299 cal bp; 550 bc-ad 651), particularly the Achaemenid Empire (2,500–2,280 cal bp; 550–330 bc). Scattered pistachio-almond scrub combined with Quercus brantii was the main vegetation type of the basin during the period studied. The present study depicts a significant increase in agriculture, suggesting urban development during the Late Antiquity and early Islamic Iranian dynasties. The inferred chronology of arboricultural activities is compatible with historical evidence showing that Fars Province witnessed economic and agricultural flourishing during these periods. The presence of the ‘Persian gardens’ is supported by the co-increase of cypress tree pollen frequencies with pollen of other cultivated trees, especially Platanus; both trees were cultivated for their shade and symbolic values. This study also provides pollen evidence of Punica granatum during the Achaemenid period and Phoenix dactylifera cultivation during the early post-Sasanian era. The variations in indicator pollen ratios among Poaceae, Artemisia, and Amaranthaceae appear compatible with the palaeohydrology of the basin and show periods of aridity followed by higher moisture availability. We suggest that anthropogenic activities played the leading role in vegetation change in the Maharlou Lake basin enhanced by climatic changes during the last ~4,000 years.