Anthropogenic inputs of nitrogen (N), phosphorus (P) and oxygen-consuming material to aquatic ecosystems can change nutrient dynamics, deplete oxygen, and change abundance and diversity of aquatic plants and animals. The Northern Rivers Ecosystem Initiative required a research and assessment program to establish the contribution of pulp mill and sewage discharges to eutrophication and depressions in dissolved oxygen (DO) in the Athabasca and Wapiti rivers of northern Alberta, Canada and examine the adequacy of existing guidelines for protecting these systems. Analysis of long-term data showed that total N (TN) and total P (TP) concentrations in exposed river reaches exceeded concentrations in reference reaches by < or = 2 times for the Athabasca River, and by 9.6 (TP) and 2.6 (TN) times for the Wapiti River. Results from nutrient limitation experiments conducted in situ and in mesocosms showed that benthic algal production was nutrient sufficient downstream of pulp mill discharges but constrained in upper river reaches by insufficient P (Athabasca River) or N + P (Wapiti River). Dissolved oxygen (DO) concentrations in both rivers declined during winter such that median concentrations in the Athabasca River 945 km downstream of the headwaters were approximately 8 mg L(-1) in mid-February. Although water column DO rarely approached the guideline of 6.5 mg L(-1), DO studies undertaken in the Wapiti River showed that pore water DO often failed to meet this guideline and could not be predicted from water column DO. Results from this integrated program of monitoring and experimentation have improved understanding of the interactions between nutrients, DO and aquatic ecosystem productivity and resulted in recommendations for revisions to nutrient and DO guidelines for these northern rivers.