High levels of ammonium in water can compromise the ecological environment and be harmful to human beings. It is of great significance to understand the source and controlling factors of ammonium in waters. However, the distribution and controlling factors on ammonium in the central Yangtze River Basin have been rarely reported. The results showed that 6.58% of the surface water (SW) exceeded the China national guideline of category III for NH4+-N (i.e., 1.0 mg/L) and 30.19% of the groundwater (GW) exceeded the China national guideline of category III for NH4+-N (i.e., 0.5 mg/L). Notably, the ammonium concentrations of the plain area in the middle were much higher, which reached to the highest value at the junction of the Yangtze River and Dongting Lake. Nitrogen in SW may originate from manure but more nitrogen sources in GW. The net anthropogenic nitrogen input (NANI) can provide enough organic nitrogen for the mineralization. NH4+-N in SW was more affected by fertilizer nitrogen and feed nitrogen input but more affected by agricultural nitrogen fixation in GW. Agricultural and industrial activities controlled NH4+-N in SW and GW by increasing nitrogen input and changing hydrological conditions. In general, this research exposed the controlling of different types of factors on ammonium in waters, providing a guidance for the water pollution prevention in study area.