Two sets of PHREEQC input and output files are provided that illustrate the distribution of aqueous ammonium and ammonia as a function of physical (temperature) and chemical (pH and solution composition) conditions. One set of simulations calculates the distribution of aqueous ammonia and aqueous ammonium over a range of temperatures and pH values in different solution compositions. The other set of simulations illustrates how aqueous ammonia concentrations in a water body change over time owing to changes in pH and temperature, how ammonia concentrations potentially toxic to salmonids (trout and salmon) can occur owing to changes in pH and temperature, and how these changes in ammonia concentration can be calculated from "continuous" records of pH and temperature provided by sensors. The ammonia concentrations toxic to salmonids are based on recommendations from the U.S. Environmental Protection Agency (EPA). The model data generated with these simulations were used to prepare selected figures in Edwards, Thea M., Puglis, Holly J., Kent, Douglas B., López Durán, Jonathan, Bradshaw, Lillie, Farag, Aïda M., Ammonia and Aquatic Ecosystems – A Review of Global Sources, Biogeochemical Cycling, and Effects on Fish, Science for the Total Environment, in review. Detailed instructions on how to download the software (PHREEQC), to run the files, and to generate the model data are provide in three read-me files. The top-level readme file (Top-level_read_me_Ammonium_Speciation_computation_files.txt) has a summary description of the data release; description of the contents; description of the software; instructions for installing the software; instructions for running the software to generate the model data; instructions for reading the output file containing the model data; acknowledgements; and a list of references. The read-me file Read-me_Ammonia_Speciation_vs_pH_temperature.txt provides a description of the simulations used to illustrate the fraction of total dissolved ammonium present as ammonia over a range of pH values and temperatures at three different solution compositions. The read-me file Read-me_Compare_ammonia_concentrations_to_EPA_Acute_CMC.txt provides a description of the simulations used to compare ammonia concentrations calculated from stream-water chemistry, including a large number of pH and temperature measurements provided by a sensor, with ammonia concentrations that are potentially toxic to salmonids.