Temperature directly affects the numeric standards for ammonia in warm-water streams of Colorado, but temperature also can affect ammonia standards indirectly through interactions that link climate, metabolic processes, and pH. Recent monitoring data for rivers on the plains of Colorado, in combination with results of studies of oxygen metabolism, suggest that the balance between photosynthesis and respiration favors high pH when temperature is high. Samples and field measurements were collected between July 2010 and May 2011 at four stations, in order to determine the relative importance of temperature, hydrologic variables, and biomass of benthic algae in controlling pH in Plains streams and rivers. Across the sampling stations, biomass of benthic algae remained low when depth was greater than ~0.35 m; below this depth threshold, algal biomass was able to accumulate when other factors were not limiting to growth. For a given location, the depth threshold of ~0.35 m can be translated into a discharge threshold for removal of algal biomass, thus providing a basis for analysis of historical records or for modeling. The potential for metabolic control of pH is highest at low discharge and especially after extended periods of low discharge. Neural-network modeling showed, for a given location, a strong relationship between discharge and pH. Temperature, time of day, and recovery (time since a critical flow for removal of periphyton biomass) affect pH at low discharge, but not when discharge is high. Although additional field studies are needed to improve modeling accuracy, these relationships demonstrate strong potential for predictions of the effects of climate variation or changes in water management on pH in Plains rivers. Preliminary modeling suggests that climate warming may lead to a modest increase in pH for Plains rivers. The most important factors affecting pH, however, are related to hydrologic variation and changes in water management, both of which can affect the patterns of accumulation for periphyton biomass.