Ammonium nitrogen contamination is one of the major problems of the Yellow River in China. The speciation, concentration and sources of nitrogen compounds as well as the water environment conditions of the Yellow River had been analyzed to study the reasons for the fact that the ammonium nitrogen concentration was above the water quality standard. In addition, laboratory experiments had been carried out to investigate the effects of suspended sediment (SS) on nitrification rate. The results indicated that the presence of SS could accelerate the nitrification process, therefore, the effects of SS on nitrification rate was not the reason for the high level of ammonium nitrogen in the river. The excessive and continuous input of nitrogen contaminants to the river was the fundamental reason for the high concentration of ammonium nitrogen. Organic and ammonium nitrogen with high concentration inhibitted the nitrification processes. When the initial NH4+ -N concentrations were 10.1, 18.4 and 28.2 mg/L, nitrification efficiencies were 17.4%, 13.0% and 2.5%, respectively. When the initial organic nitrogen concentrations were 5.5 and 8.6 mg/L, the maximum concentrations of ammonium nitrogen produced by the oxidation of organic nitrogen would reach 0.47 and 1.69 mg/L and they would last for 2 days and 6 days, respectively. The oxygen-consuming organics and toxic substance existing in the river water could inhibit the activity of nitrifying bacteria, and thus lead to the accumulation of ammonium nitrogen. In addition, the high pH value of river water resulted in the high concentration of nonionic ammonium nitrogen which would reduce the activity of nitrifying bacteria and decrease the nitrification rates. Besides, low river runoff, low SS content and low activity of nitrifying bacteria resulted in the high level of ammonium nitrogen of the river in the low water season.