After leaving its headwaters at Baltimore Lake, an alpine glacial lake, it flows due north for less than a mile and enters French Lake Reservoir — a man-made lake created by French Lake Dam, which was first constructed in 1859, reconstructed in 1948, and is managed by the Nevada Irrigation District. After flowing 1.2 miles to the northwest below the dam, Canyon Creek enters its second man-made reservoir — Faucherie Lake. Then, 1.4 miles further northwest, it enters the third of four man-made reservoirs, this time Sawmill Lake, before continuing another mile to the northwest and entering the largest of the four man-made reservoirs — Bowman Lake.
Canyon Creek then proceeds to plunge nearly 3,000 feet in elevation in just 9.1 miles through a steep canyon before its mouth at the South Yuba River at an elevation of 2,800 feet just 2.6 miles due east of the town of Washington, California.