Triplicate experimental cores and reference cores were collected from the North and South Eastern Gotland Basins. The oxygenation of the water column took place over a 96-hour experiment in a dark and 5 °C environment. In 12 and 24 hour intervals, the surface waters were exchanged and, over time, analyzed for pH, electroconductivity (EC), total organic carbon (TOC), soluble metal concentrations, and the top samples (0–10 cm) were analyzed with 3-step (E1: water-soluble, E2: exchangeable, and E3: organic-bound) sequential chemical extraction (SCE). Results show stable pH and decreasing EC in the column waters. The EC indicates that metals are released in the initial phases (12 h) of reoxygenation for both sites. Arsenic, Ba, Co, Mn, Rb, U, K, Sr, and Mo are released into the water column during the 96 hour experiment, and based on the calculations for the entire East Gotland Basin, would mean 8, 50, 0.55, 734, 53, 27, 347,178, 3468, and 156 μg L−1 are released, respectively. Elements Mn, Mo, U, and As are released in higher concentrations during the experiment than previously measured in the Eastern Gotland Basin, which provides vital information for future proposed remediation and natural geochemical processes with their known environmental impacts. The SCE results show that redox-sensitive metals (Mn, U, and Mo) are released in the highest concentrations into the solution. The relationship between the highest released metals (beside redox-sensitive) into solution over the oxygenation and their initial abundant phase is noticed, where the smallest released concentrations belong to K < Rb < Sr in E2, and As<Ba in E3, respectively.