[8] In 2001, the Central Valley Regional Water Quality Control Board and the U.S. Geological Survey confirmed that Cache Creek was a contributor to the increase of mercury levels within the Sacramento River.

[9] Since then, various regulations have been enacted to monitor the mercury levels in Cache Creek, and multiple studies have been conducted to find the site of contamination.

The California Office of Environmental Health Hazard Assessment released an advisory regarding eating fish caught from this creek based on the mercury level.

It then flows south along New Long Valley Road, and turns east along State Route 20, which it crosses at the Cache Creek Recreation Area.

Under the Solano Decree Yolo currently holds appropriative rights for up to 150,000 acre-feet (190,000,000 m3) per year from Clear Lake, and all the water from the Indian Valley dam.

There is a rock ledge a mile and a half downstream of Clear Lake, called the Grigsby Riffle, near the bridge on State Route 53.

The bottleneck is seen as a backup to prevent flooding downstream and Yolo County is prohibited from increasing the capacity of the channel by the Gopcevic and Bemmerly Decrees.

[15][16] From the early 1800s to much of the 1900s, mining for elemental mercury, also known as quicksilver, was widely popular in Cache Creek's upper watershed, given its gold recovering properties.

[18] Throughout this period, little to no environmental regulations had been established causing mercury, in the form of mining waste from retorting, to infiltrate water systems and make its way into Cache Creek .

[17] If consumed, accumulation of high mercury levels within organisms, particularity fish, may induce harm to the nervous systems of unborn babies and young children.

[21] Reports like this led to protocols set in place to monitor the mercury levels within Cache Creek and warn the public of possible health concerns from fish consumption.

In 2017, The Department of Environmental Science and Policy from UC Davis, in consultation with The Yolo County Cache Creek Technical Advisory Committee, proposed revisions to the existing protocols.

Whitewater boating on Cache Creek includes kayaking, rafting, canoeing and innertubing which are popular in the summer using the water released from the dams for downstream agriculture.

[23][24] Nominally a tributary of the Sacramento River, Cache Creek now only reaches it during extremely wet years due to damming and diversion of the stream's water.

Degradation of the channel caused by invasive plants, such as Arundo donax and Tamarix spp., as well as gravel mining has left no suitable habitat for Chinook salmon and steelhead to spawn, even if there is enough water.