Putah Creek is a major stream in Northern California, a tributary of the Yolo Bypass. The 85-mile-long (137 km) creek has its headwaters in the Mayacamas Mountains, a part of the Coast Range. The true meaning of "Putah" in Putah Creek has been the subject of discussion and speculation.
The creek originates from springs on the east side of Cobb Mountain south of the town of Cobb in southwestern Lake County. It descends eastward to the town of Whispering Pines, where it turns southeast, parallelling State Route 175. It passes the town of Anderson Springs, where it joins Bear Canyon Creek. North of Middletown, it curves counterclockwise around Harbin Mountain, merging in close succession with Dry Creek, Helena Creek, Crazy Creek, Harbin Creek, and Big Canyon Creek. From Harbin Mountain, it flows east again, joining Bucksnort Creek, then enters Napa County at a confluence with Hunting Creek about 11 mi (18 km) east of Middletown. In Napa County, the creek flows southeast, merging with Butts Creek just before it empties into Lake Berryessa.

Downstream of Monticello Dam, on the southeastern corner of the lake, Putah Creek leaves Napa County and becomes the boundary between Yolo County and Solano County. In this section it offers excellent fishing opportunities year round. California Department of Fish and Wildlife regulations require "catch and release" in this section of the stream, as well as the use of artificial lures with barbless hooks. The stream continues east along State Route 128, receiving Pleasants Creek before arriving at Lake Solano where the Putah Diversion Dam diverts flows to the Putah South Canal, carrying water to the residents of Vallejo. Below Lake Solano, Putah Creek receives McCune Creek, then its last tributary, Dry Creek. After the Dry Creek confluence it passes through the town of Winters to reach Interstate 505. From there Putah Creek channel continues eastward, parallelling Putah Creek Road to Stevenson Bridge Road.
Putah Creek used to flow near downtown Davis in what is now the UC Davis Arboretum channel, but early settlers redirected the creek south of Davis in 1871, and in the late 1940s the Army Corps of Engineers added levees to what is now the South Fork Putah Creek. A few miles east of Davis, the county line turns south, but the South Fork Putah Creek continues eastward, passing south of Davis to feed into the Yolo Bypass about a quarter mile (400 m) west of the Sacramento Deep Water Channel.

Steelhead trout (coastal rainbow trout) (Oncorhynchus mykiss irideus) and Chinook salmon (Oncorhynchus tshawytscha) continue to survive in Putah Creek. Although these anadromous salmonids cannot pass the Putah Diversion Dam, stream resident rainbow trout continue to thrive above Monticello Dam in the upper headwaters and grow to large size in the first few miles directly below the dam. In December 2014, the California Fish and Game Commission designated Putah Creek a "Wild Trout Water" and efforts by citizen groups to restore the creek appear to be resulting in increased salmon rearing in the lower watershed.