Marsh is an important wetland type in Hengduan Mountain area (HMA). To explore the distribution and control factors of total nitrogen (TN), nitrate nitrogen (NN), and ammonias nitrogen (AN) in water of marshes across HMA, water samples were taken and analyzed during 2014-2017. Meanwhile, environmental data, including precipitation, air temperature, water temperature, water depth, population, gross domestic product (GDP), and number of livestock were collected as well. The results showed that: 1) the content of TN in water of marshes followed the law of latitudinal zonality and vertical zonality, i.e., the content of TN decreased with the increase of latitude and altitude across the HMA. Water temperature was a control factor of the distribution of TN along the latitude and altitude. Meanwhile, the content of TN increased with the increase of longitude, which may drive by socio-economic factors. 2) The contents of NN and AN in water of marshes did not change significantly along the altitude in the HMA. 3) The contents of NN in water of marshes increased with the increase of longitude and latitude across the HMA. Water depth and water temperature were drivers of this distribution. 4) The content of AN in water of marshes increased with the increase of longitude across the HMA. However, the distribution of AN could not be well explained by the natural and socio-economic factors.