The Portneuf River, Idaho, is heavily impacted by human land use and consequently experiences high nutrient loading to some reaches. We examined how nitrogen and phosphorus concentrations changed along the mainstem river, and whether these changes were related to ecosystem function measures during Aug-Oct 2006. Six study sites were distributed 17–70 km above a terminal reservoir. Total and dissolved nitrogen and phosphorus loads were constant and low between river kilometers (RK) 20–70, but were 3–1000 fold greater at the RK 17 site, which experiences nutrient-rich groundwater input. Nutrient diffusing substrate (NDS) bioassays showed that periphyton biomass and net ecosystem production was not nutrient limited at most study sites and did not appear to be related to nutrient loads. Ecosystem respiration was not nutrient limited but was greatest on NDS at the RK 17 site. Organic matter processing potential, measured using leaf pack decay, was also greatest at the RK 17 site and showed little variation among other sampling sites. In conclusion, we found that relationships between water chemistry and ecosystem function measures varied depending on the metric of interest, and may provide complimentary, although sometimes contradictory, conclusions concerning ecosystem integrity in large, nutrient rich rivers.