Increasing volumes of treated and untreated human sewage discharged into rivers around the world are likely to be leading to high aquatic concentrations of toxic, un-ionized ammonia (NH3), with negative impacts on species and ecosystems. Tools and approaches are needed for assessing the dynamics of NH3. This paper describes a modeling approach for first-order assessment of potential NH3 toxicity in urban rivers. In this study daily dissolved NH3 concentrations in the Rio Grande of central New Mexico, USA, at the city of Albuquerque's treated sewage outfall were modeled for 1989–2002. Data for ammonium (NH4+) concentrations in the sewage and data for discharge, temperature, and pH for both sewage effluent and the river were used. We used State of New Mexico acute and chronic NH3-N concentration values (0.30 and 0.05 mg/L NH3-N, respectively) and other reported standards as benchmarks for determining NH3 toxicity in the river and for assessing potential impact on population dynamics for fish species. A critical species of concern is the Rio Grande silvery minnow (Hybognathus amarus), an endangered species in the river near Albuquerque. Results show that NH3 concentrations matched or exceeded acute levels 13%, 3%, and 4% of the time in 1989, 1991, and 1992, respectively. Modeled NH3 concentrations matched or exceeded chronic values 97%, 74%, 78%, and 11% of the time in 1989, 1991, 1992, and 1997, respectively. Exceedences ranged from 0% to 1% in later years after enhancements to the wastewater treatment plant. Modeled NH3 concentrations may differ from actual concentrations because of NH3 and NH4+ loss terms and additive terms such as mixing processes, volatilization, nitrification, sorbtion, and NH4+ uptake. We conclude that NH3 toxicity must be considered seriously for its potential ecological impacts on the Rio Grande and as a mechanism contributing to the decline of the Rio Grande fish community in general and the Rio Grande silvery minnow specifically. Conclusions drawn for the Rio Grande suggest that NH3 concentrations may be high in rivers around the world where alkaline pH values are prevalent and sewage treatment capabilities are poorly developed or absent.