The Lower Jordan River is located in the semiarid area of the Jordan Valley, along the border between Israel and Jordan. The implementation of the water sections of the peace treaty between Israel and Jordan and the countries' commitment to improve the ecological sustainability of the river system require a better understanding of the riverine environment. This paper investigates the sources and transformations of nitrogen compounds in the Lower Jordan River by applying a combination of physical, chemical, isotopic, and mathematical techniques. The source waters of the Lower Jordan River contain sewage, which contributes high ammonium loads to the river. Ammonium concentrations decrease from 20 to 0-5 mg N L(-1) along the first 20 km of the Lower Jordan River, while nitrate concentrations increase from nearly zero to 10-15 mg N L(-1), and delta(15)N (NO(3)) values increase from less than 5 per thousand to 15-20 per thousand. Our data analysis indicates that intensive nitrification occurs along the river, between 5 and 12 km from the Sea of Galilee, while further downstream nitrate concentration increases mostly due to an external subsurface water source that enters the river.