Developing management strategies to safeguard public health and environmental sustainability requires a comprehensive understanding of the solubility and mobility of trace and alkaline metals in the event of seawater flooding. This study investigated the effects of seawater flooding, along the duration of flooding, on the release of trace and alkaline metals (Mn, Fe, Cu, Zn, Ca, K, and Mg) in two calcareous soils (Krome and Biscayne) located in southern Florida. Seawater flooding experiments involved two soil types and four flooding durations (1, 7, 14, and 28 days) replicated three times. Freshwater flooding experiments were also conducted for comparison. After each flooding experiment, soil samples were collected at three depths (15, 30, and 45 cm), and analyzed for selected elements. Comparative analysis revealed significant releases of Mn, Fe, and Zn in both soils flooded by seawater compared to freshwater. In most cases, significant increments were evident as early as 1-day exposure to seawater flooding, which further increased with flooding duration. However, the impacts of seawater flooding had notable differences between the two soils. Seawater flooding in Krome soil for 28 days, resulted in higher Mn, Fe, and Zn contents by 58, 340, and 510% compared with freshwater flooding, while corresponding increases in Biscayne soil were 3.3, 130, and 180%, respectively. Comparable marginal increases in Cu content were observed for both soils. Similarly, seawater flooding increased K, Mg, and Na contents from single-day flooding. The interplay between soil type, column depth, flooding duration, and their interactions proved influential factors in determining Mn, Fe, Cu, and Zn releases, with peak levels typically observed on the 28th day of flooding and at bottom depths. Overall, these findings highlight the release of these elements, raising concerns about potential plant toxicity and groundwater or surface water contamination due to leaching and runoff.