River ecosystems are significantly affected by various heavy metal pollutants generated through anthropogenic activities, posing global environmental challenges. Sediment contamination in rivers is a critical concern due to its toxicity and bioaccumulation. Heavy metal leaching can occur, thereby affecting the final use of sediments. The transition of arsenic (As), zinc (Zn), and nickel (Ni) fractions formed in sulfide-rich sedimentary deposits was conducted using SM&T sequential extraction. The results for residential and industrial areas showed a notable shift caused by hydrothermal technology (HTT). Specifically, we observed a significant shift in binding forms from fractions 1 and 2, associated with a high potential for natural leaching, to fractions 3 and 4, where leaching under environmental conditions was nearly negligible. The ratio of the residual fraction increased with hydrothermal treatment, and the pyrolysis temperature was transferred to the oxidative and residual fractions, stabilizing the heavy metals.