Nitrogen and phosphorus criteria were developed for 233 km of the Yellowstone River, one of the first cases where a mechanistic model has been used to derive large river numeric nutrient criteria. A water quality model and a companion model which simulates lateral algal biomass across transects were used to simulate effects of increasing nutrients on five variables (dissolved oxygen, total organic carbon, total dissolved gas, pH, and benthic algal biomass in depths ≤1 m). Incremental increases in nutrients were evaluated relative to their impact on predefined thresholds for each variable; the first variable to exceed a threshold set the nutrient criteria. Simulations were made at a low flow, the 14Q5 (lowest average 14 consecutive day flow, July-September, recurring one in five years), which was derived using benthic algae growth curves and EPA guidance on excursion frequency. An extant climate dataset with an annual recurrence was used, and tributary water quality and flows were coincident with the river's 10 lowest flow years. The river had different sensitivities to nutrients longitudinally, pH being the most sensitive variable in the upstream reach and algal biomass in the lower. Model-based criteria for the Yellowstone River are as follows: between the Bighorn and Powder river confluences, 55 lg TP/l and 655 lg TN/l; from the Powder River confluence to Montana state line, 95 lg TP/l and 815 lg TN/l. Pros and cons of using steady-state models to derive river nutrient criteria are discussed.(KEY TERMS: algae; large river; nutrients; water quality criteria; model; environmental impacts; environmental regulations; QUAL2K; Yellowstone River; eutrophication.) Suplee, Michael W., Kyle F. Flynn, and Steven C. Chapra, 2015. Model-Based Nitrogen and Phosphorus (Nutrient) Criteria for Large Temperate Rivers: 2. Criteria Derivation.