In conjunction with the extensive archaeological projects conducted at the current outlet of Sweden’s second largest lake, Lake Vättern, macrofossil, pollen and diatom records have been studied from ¹⁴C-dated lake and river sediments from River Motala Ström in Motala and Lake Boren. These investigations have revealed sedimentary evidence of the Yoldia Sea regression, the Ancient Lake Vättern transgression, and the following stepwise river formation process. Around 9000 cal BC, two small kettlehole basins at Strandvägen and Kanaljorden became isolated from the Baltic basin. As the ice sheet retreated further north, the isostatic uplift isolated the Vättern basin from the Baltic basin. Due to the uneven isostatic uplift, the basin tilted toward the south, and the Ancient Lake Vättern transgression started in Motala. The threshold in Motala at 92.5 m a.s.l. was reached around 7200 cal BC, and River Motala Ström was formed. ¹⁴C-dated diatom records from Lake Boren, and shoreline deposits in Motala, confirm this event. The water level in Lake Vättern initially fell around 1.5 m, and around 5800 cal BC, a second erosional event cut down the threshold to modern day level. At this time, the Late Mesolithic settlements in Motala were established and expanded.