Malodorous rivers are among the major environmental problem of cities in developing countries. In addition to the unpleasant smell, the sediments of such rivers can act as a sink for pollutants. The excessive amount of ammonia nitrogen (NH3−N) in rivers is the main factor that causes the malodor. Therefore, a suitable method is necessary for sediment disposition and NH3−N removal in malodorous rivers. The sediment in a malodorous river (PS) in Beijing, China was selected and modified via calcination (PS-D), Na+ doping (PS-Na), and calcination−Na+ doping (PS-DNa). The NH3−N removal efficiency using the four sediment materials was evaluated, and results indicated that the NH3−N removal efficiency using the modified sediment materials could reach over 60%. PS-DNa achieved the highest NH3−N removal efficiency (90.04%). The kinetics study showed that the pseudo-second-order model could effectively describe the sorption kinetics and that the exterior activated site had the main function of P sorption. The results of the sorption isotherms indicated that the maximum sorption capacities of PS-Na, PS-D, and PS-DNa were 0.343, 0.831, and 1.113 mg g−1, respectively, and a high temperature was favorable to sorption. The calculated thermodynamic parameters suggested that sorption was a feasible or spontaneous (ΔG < 0), entropy-driven (ΔS > 0), and endothermic (ΔH > 0) reaction.