In 1998, the U.S. Geological Survey sampled the Clackamas River, its major tributaries, and reservoirs to characterize basic water quality (nutrients, dissolved oxygen, pH, temperature, and conductance), water quantity (water sources within the basin), and algal conditions (biomass and species composition). Sampling locations reflected the dominant land uses in the basin (forest management, agriculture, and urban development) as well as the influence of hydroelectric projects, to examine how these human influences might be affecting water quality and algal conditions. Nuisance algal growths, with accompanying negative effects on water quality, were observed at several locations in the basin during this study. Algal biomass in the lower Clackamas River reached a maximum of 300 mg/m2 chlorophyll a, producing nuisance algal conditions, including fouled stream channels and daily fluctuations in pH and dissolved oxygen concentrations to levels that did not meet water-quality standards. Algal biomass was highest at sites immediately downstream from the hydroelectric project's reservoirs and/or powerhouses. Nuisance algal conditions also were observed in some of the tributaries, including the North Fork of the Clackamas River, Clear Creek, Rock Creek, and Sieben Creek. High amounts of drifting algae increased turbidity levels in the Clackamas River during June, which coincided with a general increase in the concentration of disinfection by-products found in treated Clackamas River water used for drinking, presumably due to the greater amounts of organic matter in the river. The highest nutrient concentrations were found in the four lowermost tributaries (Deep, Richardson, Rock, and Sieben Creeks), where most of the agriculture and urban development is concentrated. Of these, the greatest load of nutrients came from Deep Creek, which had both high nutrient concentrations and relatively high streamflow. Streams draining forestland in the upper basin (upper Clackamas River and Oak Grove Fork) had the highest concentrations of phosphorus (and lowest concentrations of nitrogen), and streams draining forestland in the middle basin (Clear Creek, Eagle Creek, and the North Fork of the Clackamas River) had relatively high concentrations of nitrogen (and low concentrations of phosphorus). In contrast, relatively low concentrations of both nitrogen and phosphorus were found at the two reference streams, reflecting their pristine condition. Relatively high phosphorus levels in the upper basin are probably due to the erosion of naturally occurring phosphorus deposits in this area. Likely sources of nitrogen (mostly nitrate) in the forested watersheds include nitrogen-fixing plants, atmospheric deposition, timber harvesting, and applications of urea fertilizers.