This study focuses on the treatment of heavy metal ions and achieving enhancement of river sediment, which is rich in organics. Fulvic acid was used as the main representative of organics in which to study the transfer of Cu2+, Zn2+ ions in the electroosmotic system, in both the absence and presence of organics. In addition, the effects of the experiment parameters (i.e., voltages, displacement, and water content), heavy metal ion content (0.19% and 0.38%, respectively), and the concentration of organics (1.5%, 3%, and 4.5%) acting on migration of ions and physiochemical properties of sediment, before and after electro-osmosis treatment were investigated. Mineral composition of the soil and its microscopic characteristics were analyzed by scanning electron microscopy. The results show that the 4.5% fulvic acid added in the sediment can enhance the migration ability of Cu2+ and Zn2+ ions through complexation, and simultaneously effectively reduce the formation of colloids with the average reductions of Cu2+ ions and Zn2+ ions being 28 and 11 mg/kg, respectively. While the dewatering capacity of the sediment with higher fulvic acid content is weaker, fulvic acid can effectively reduce the corrosion of the electrode during the electro-osmosis process, due to the film formed on the metal surface. Moreover, the fulvic acid in the organics can be combined with the aluminum and calcium produced by the hydration of the cement, delaying the hydration of the cement, while simultaneously decomposing the hydration product and hindering the hardening of the cement, thereby affecting and destroying the formation of the sediment’s structure and its strength.