The continuous release of nutrients from sediment is a major barrier to the remediation of black odorous rivers. This study used a long-term laboratory incubation experiment to investigate the effectiveness of sediment dredging, intermittent aeration, and in situ inactivation with modified clays to reduce the internal loading of sediment from a seriously polluted river. The results indicated that intermittent aeration and in situ inactivation were effective in reducing the TN and NH₄⁺ concentrations in the water column. However, sediment dredging did not consistently reduce the TN and NH₄⁺ concentrations in the water column. In contrast, the three methods were all effective in controlling the TP and PO₄³⁻ concentrations in the water column. Except for dredging, >30% of NH₄⁺ and 40% of PO₄³⁻ fluxes from sediment were reduced when compared with a control sample after 120 days of remediation. Dredging induced a significant release of NH₄⁺ from sediment. Dredging and aeration made nearly no change to the amount of extractable nitrogen in the sediment. However, inactivation may increase sediment-extractable ammonium in deep sediment layers with time due to vertical transportation of clay by intensive bioturbation. Dredging is the most effective way to reduce surface mobile phosphorus over time while the transported clays can reduce a large percentage of the mobile phosphorus in deeper sediment. The relative abundance of Nitrospira in the surface sediment increased significantly with each remediation measure, creating favorable conditions for the reduction of the ammonium released from sediment. Altogether, the results of this study indicated that clay inactivation is the best method for controlling the internal loading of both phosphorus and nitrogen in seriously polluted river sediment.