The system was primarily developed to control floods, provide water for irrigation, and serve the hydropower system by storing water for use when power demand is high. Little is known about survival rates of salmon once they enter the Pacific Ocean, but there is growing evidence that survival rates are not uniform from year to year and that variations in ocean productivity may affect stocks over wide geographic areas and time frames. Annual variability and the possibility of long-term trends in the ocean environment make it difficult to detect changes in survival that result from efforts to improve inland conditions. When salmon begin their upstream migration as adults, they face harvest by commercial and recreational fisherman and predation by marine mammals and other animals. Passage through the dams also presents a problem.
Biologists are able to count salmon as they use the dams' fish ladders on their way upstream.
When the adult salmon return to the area where they emerged from their parents' redd, they again face habitat problems. Spawning beds may be silted in with sediment from logging, mining, or road building, or the water may be too warm for them. In addition, the human activities may unintentionally scare them away from the spawning beds.