is it a polluted river?
Yes, agricultural runoff from farms and ranches in the Snake River Plain and many other areas has severely damaged the ecology of the river throughout the 20th century.
Snake River
Agricultural runoff from farms and ranches in the Snake River Plain and many other areas has severely damaged the ecology of the river throughout the 20th century. 
does the snake river flow into the columbia river No, it is a tributary of the latter, and flows into the Pacific Ocean.
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Snake River [SEP] Pollution
In December 2007, the U.S. Environmental Protection Agency (EPA) issued a permit requiring owners of fish farms along the Snake River to reduce their phosphorus discharge by 40%. Pollutant levels in Hells Canyon upstream of the Salmon River confluence, including that of water temperature, dissolved nutrients, and sediment, are required to meet certain levels.