This paper describes the analyses of pollen, non-pollen palynomorphs, macroremains and geochemistry in sediments from archaeological excavations at Wyspa Spichrzow (“Granary Island”) in Gdansk, northern Poland. The aim of this study was to reconstruct the environmental conditions in this part of the town in the period preceding its occupation and during its transformation with the establishment of a trade centre and an increasing number of granaries, warehouses and workshops. The results show that this area was originally covered by wetlands typical of river oxbows, with a landscape formed by alder woods, shallow pools of water, fens and patches of wet meadows. Around the 9th–10th centuries, a distinct lowering of the groundwater table reduced the pools, and the alder stands also reduced. These changes coincided with the Medieval Climatic Anomaly. Drying of the ground could have been an important factor enabling expansion of settlement in the Gdansk area. Between the 10th and 13th–14th centuries, the area around the investigated sites was probably used as pasture, as shown by high frequencies of coprophilous fungal spores. A large representation of cereal pollen and pollen and macroremains of field weeds reflects crop transport and storage on the island from ca. the 13th/14th centuries in the northern part of the area and the 15th/16th centuries in its southern part. The increasing human impact caused development of a rich flora associated with human activities, habitat enrichment by nitrogen and phosphorus, and heavy metal pollution from the beginning of the 13th century.