A hydrodynamic, water temperature, and water-quality model of the Link River to Keno Dam reach of the upper Klamath River was updated to account for macrophytes and enhanced pH buffering from dissolved organic matter, ammonia, and orthophosphorus. Macrophytes had been observed in this reach by field personnel, so macrophyte field data were collected in summer and fall (June-October) 2011 to provide a dataset to guide the inclusion of macrophytes in the model. Three types of macrophytes were most common: pondweed (Potamogeton species), coontail (Ceratophyllum demersum), and common waterweed (Elodea canadensis). Pondweed was found throughout the Link River to Keno Dam reach in early summer with densities declining by mid-summer and fall. Coontail and common waterweed were more common in the lower reach near Keno Dam and were at highest density in summer. All species were most dense in shallow water (less than 2 meters deep) near shore. The highest estimated dry weight biomass for any sample during the study was 202 grams per square meter for coontail in August. Guided by field results, three macrophyte groups were incorporated into the CE-QUAL-W2 model for calendar years 2006-09. The CE-QUAL-W2 model code was adjusted to allow the user to initialize macrophyte populations spatially across the model grid. The default CE-QUAL-W2 model includes pH buffering by carbonates, but does not include pH buffering by organic matter, ammonia, or orthophosphorus. These three constituents, especially dissolved organic matter, are present in the upper Klamath River at concentrations that provide substantial pH buffering capacity. In this study, CE-QUAL-W2 was updated to include this enhanced buffering capacity in the simulation of pH. Acid dissociation constants for ammonium and phosphoric acid were taken from the literature. For dissolved organic matter, the number of organic acid groups and each group's acid dissociation constant (Ka) and site density (moles of sites per mole of carbon) were derived by fitting a theoretical buffering response to measured upper Klamath River alkalinity titration curves. The organic matter buffering in the Klamath River was modeled with two monoprotic organic acids: carboxylic acids with a mean pKa of 5.584 and site density of 0.1925, and phenolic organic acids with a mean pKa of 9.594 and site density of 0.6466. Total inorganic carbon concentrations in the model boundary inputs were recalculated based on the new buffering equations. CE-QUAL-W2 was also adjusted to allow the simulation of nonconservative alkalinity caused by nitrification, denitrification, photosynthesis, and respiration. The Klamath River model was recalibrated after the macrophyte and pH buffering updates producing improved predictions for pH, dissolved oxygen, and particulate carbon.