[7] Clear Lake supports large populations of largemouth bass, crappie, bluegill, carp and catfish.

[13][14] The California Office of Environmental Health Hazard Assessment released an advisory statement regarding eating fish caught from the lake, based on the mercury level.

[15][16] The Clear Lake basin attracts large quantities of waterfowl, including mallards, western grebe, coots, various species of geese, ospreys, plovers, mergansers and many others.

Much of the shoreline is developed, but parks, reserves, miles of open water and private land also exist allowing many opportunities for observing and enjoying nature.

The county also hosts a growing population of the rare tule elk, recently reintroduced after being locally hunted to extinction one hundred years before.

[18] Along the shoreline and creeks, there are aquatic growths of tule, cattail, willow, cottonwood, box elder, and many other types of riparian plant life.

This species of "phantom midge" (so called because the larvae are transparent and very difficult to see) measures less than 1⁄4 inch (6.4 mm) long and resembles a tiny mosquito, but is non-biting.

The rugged coastal mountains surrounding Clear Lake are covered with thick stands of oak-madrone forest, manzanita, sage shrubs, chaparral, and grasses.

The heavy forestation and ruggedness of this part of California has helped prevent wholesale real estate development or farming.

Abundant fish, game and waterbirds made Clear Lake an oasis in the otherwise harsh conditions of Northern California's mountains.

A number of Pomo were enslaved and abused by settlers, notably Andrew Kelsey (whose name is attached to the town of Kelseyville) and Charles Stone.

The following year, a United States Army contingent under Lieutenant Nathaniel Lyon cornered as many as 200 Pomo on an island in Clear Lake and slaughtered most of them—including scores of women and children.

[27] The company expressed interest in the "possibility of harvesting the county's algae for sale in specialty markets in Europe and Japan".

[26] The Clear Lake Algae Research Unit was disbanded in October 1978 for lack of funding, eight years after its start.

[29] The Clear Lake Watershed is contained within the Upper Cache Creek USGS hydrologic unit, an area that encompasses 271,360 acres (109,820 ha).

Seventy percent of the terrain has very shallow topsoil, which saturates after a rainfall of 3 to 4 inches (76 to 102 mm), after which runoff flows quickly into the lake.

The combination of rapid inflow and slow outflow results in frequent flooding of low-elevation areas such as downtown Clearlake and Lakeport.

Its level was originally controlled by a rocky ledge in Cache Creek called the "Grigsby Riffle" (which is now submerged upstream of the 1914 dam).

[40][41][42] The northern end of Clear Lake adjacent to Rodman Slough and Middle Creek was blocked off with levees between 1900 and 1940, and the land was reclaimed for agricultural use.

During the summer months, Clear Lake provides irrigation flows for agricultural operations in Yolo County.

Due to increased agricultural and urban land use, Clear Lake's historic wetland habitats have been reduced by 79%.

Other agricultural activities such as stream channelization, groundwater pumping, application of fertilizers and pesticide use have contributed to lake sedimentation, hillside erosion and floodplain encroachment.

Its population is believed to be kept in check now by two introduced fish species (the threadfin shad and the inland silverside) that compete with the gnat for its preferred zooplankton for food.

[51] The plant established so successfully due to its ability to break into smaller propagules, which can survive in sediment for up to seven years.

Studies have shown that increased nutrient contents, especially in the form of phosphorus, from fertilizer runoff can potentially influence cyanobacteria blooms[31] The California Water Boards have found that phosphorus loading in Clear Lake is largely driven by sedimentation due to erosion from agricultural activities as well as channel erosion, mining activities, wildfires, off-highway vehicle use, and timber harvesting.

[58] Types of toxin-producing cyanobacteria that have been identified in Clear Lake include the following genera: Anabaena, Microcystis, Oscillatoria, Planktothrix, Aphanizomenon, Cylindrospermopsis, and Lyngbya,[59] all of which can cause short- and long-term health effects.

In 2009 the Middle Creek and Hamilton City Flood Damage Restoration and Ecosystem Act (AB74) was signed by Governor Arnold Schwarzenegger.

The passage of Assembly Bill 707[69] allowed for the creation of the Blue Ribbon Committee for the Rehabilitation of Clear Lake.

The committee is charged with providing scientifically sound recommendations for the management of Clear Lake's "economy, ecosystem, and heritage".

[75] Within the jurisdictional boundary of the County of Lake, the Watershed Protection District provides the "Lake County Clean Water Program" for compliance with the National Pollutant Discharge Elimination System (NPDES) pollution prevention programs,[76][77] and with the NPDES stormwater management permit (issued by the State Water Resources Control Board as Water Quality Order 2013-0001-DWQ),[78] by implementing the Lake County "Stormwater Management Plan".