Press "Enter" to skip to content

Who Impairs Clear Lake?

There is no escaping the inexorable judgment of weather and time. Every year, the rain renders its verdict on the decisions industrial humans have made on the land.

During the last 150 years, those decisions in the Clear Lake basin have included the destruction of roughly 85% of the wetlands that once edged the lakeshore. It has also included clear-cut and post-fire logging in the Mendocino National Forest, one of the largest mercury mines in California, sewers and roads, wine-grape farms, cannabis farms, rice farms, cattle farms, and wildfires. And it includes dudes on dirt bikes who flock to South Cow Mountain every year by the tens of thousands, disturbing the sediment by carving out an endless maze of new roads.

I have on my laptop maps of sediment in Lake County generated by outer-space satellites. Ohio-based Blue Water Satellite Imaging acquired raw data from the United States Geological Service's Landsat 5 and Landsat 7 satellites from a day shortly after a solid early-winter storm — December 24, 2012 — and used it to track the presence of one nutrient that has been particularly troubling for the lake: phosphorus.

The company's mapmakers colored in red those areas where phosphorus levels exceed 60 parts per billion (PPB) (as compared with the 10-15 PPB the EPA commonly targets in water clean-up efforts). The largest such blotch appears on the northwestern end of the lake, near Nice and Lucerne, which receives run-off from Clear Lake's two largest tributaries: Scott Creek (with headwaters on North Cow Mountain) and Middle Creek (headwaters in the Mendocino National Forest above Upper Lake). Other notable red sediment blotches appear on Clear Lake's lower arm, where Cache Creek drains it toward the Sacramento River, and in the area adjacent to Big Valley on the lake's southwest, which is the heart of Lake County's wine-dominated agribusiness sector.

Notably, Middle and Scott Creek drain through Rodman Slough, which appears on the map as almost entirely one solid red blotch. Lake Pillsbury, which collects the headwaters of the mainstem Eel River, also consists of such a blotch. It is visible in the upper-left corner of the map. In all, roughly 9.3% of the lake's waters were in the figurative red zone on that day.

Total Phosphorus in Water. Overlay on natural color image of surrounding landscape. Clear Lake, CA, Dec 24, 2012.
Total Phosphorus in Water. Overlay on natural color image of surrounding landscape.

The dangers of elevated phosphorus or nitrogen in water are known throughout the world. Large concentrations of these nutrients in water and soil cycles lowers oxygen levels, effecting metabolism and growth of oxygen-dependent species, causing fish to suffocate and die. Examples within the US abound. In the Gulf of Mexico is a 6,900 square mile “dead zone” — about the size of New Jersey where, primarily because of nitrogen run-off from the Mississippi River, no life can survive.

Since the Great Lakes have been used as a common industrial dumping ground, less than 3% of the lakes' shorelines are now suitable for swimming, drinking, or supporting any aquatic life. The algaes that grow in Lake Erie, for instance, produce deadly liver and nerve toxins, which primarily feed off of phosphorus (about 60% of which comes from farms).

Clear Lake's Impairment

In the early-1970s, the US Congress approved a spate of legislation — the Clean Water Act, the Safe Drinking Water Act, and the Endangered Species Act — that is supposed to preserve the quality of rivers, lakes, watersheds, wetlands, natural aquifers, and other sources of fresh water. Under the Clean Water Act, the main mechanism for reducing pollution into a water body is called a TMDL: Total Maximum Daily Load, a calculation of the maximum amount of a pollutant a waterbody can receive and still safely meet healthy standards as determined by the Environmental Protection Agency (EPA).

Clear Lake's excess sediment has long been recognized. In 1986, the EPA deemed the lake an “impaired water body” The EPA delegates authority to state agencies to implement a TMDL to bring water bodies out of their “impaired” state. The Central Valley Regional Water Quality Control Board (CRWQCB) (henceforth, “Central Valley Water Board”), a division of the California Environmental Protection Agency, created a “TMDL for control of nutrients in Clear Lake” in 2006.

The Clear Lake TMDL designates "waste load allocations" to "responsible parties" (federal, irrigated, unincorporated, incorporated, and state lands — i.e., CalTrans) for reduction in the annual nutrient loading of Clear Lake. Its implementation plan directs these parties to estimate their loading to the lake and implement actions to control phosphorus. Even though most of these entities are outside of Lake County's jurisdiction, the TMDL calls upon Lake County to serve as the “lead agency” for implementing the reductions.

Yet, blue-green algae blooms have thrived in Clear Lake since the TMDL came into effect. The algae thrives in calm, warm, and nutrient-rich (ie, phosphorus-rich) waters, which the lake provides in abundance. Photosynthetic bacteria called cyanobacteria associate with the algae, lowering dissolved oxygen levels and producing toxins (cyanotoxins), which can kill wildlife and induce cancers in humans.

Sarah Ryan is the director of the Big Valley Rancheria Band of Pomo Indians’ environmental department, which has closely monitored Clear Lake’s cyanobacteria problems with a focus on cyanotoxins. In early-September, the Rancheria and the Elem Band of Pomo Indians jointly initiated a task force to coordinate the county's response to the tribes' monitoring of cyanobacteria toxins in Clear Lake, such as whether and where to post warning signs. The task force includes participants from Lake County, Clearlake (the town), Lakeport, and federal and state agencies. In the worst case, the tribes discovered Microcystis cell counts of nearly 17,000 parts per billion near Clearlake Oaks.

Microsystin is a hepatotoxin and dermatoxin that is considered the most commonly occurring class of cyanotoxin in the waters of North America, if not the world. The World Health Organization guideline for recreating in waters with microcystins is that anything over 20 ppb has a moderate risk associated with it. The California EPA's Office of Environmental Health Hazard Assessment (OEHHA) has deemed microsystin levels of 0.8 ppb as unsafe for recreating in water.

“Nowadays, Clear Lake has much more worrisome algal blooms than it did when the TMDL started in 2006,” Ryan says. “It’s really noteworthy that the levels of cyanobacteria increased a few years after the nutrient TMDL was supposed to start reducing the problem.”

Part of the problem is climate change, of course. Recent years have seen the highest average temperatures in California since official record-keeping began in the late-1870s, and cyanobacteria thrive in warm waters. But an even bigger part of the problem, critics say, has to do with the county's lack of political will, as well as a state of willful ignorance about where the pollution is coming from, which is maintained by entities like agribusiness.

The Essential Public Information Center, based in Upper Lake, has closely monitored county, state, and federal programs to improve the Clear Lake basin watershed's health for more than a decade. Its founder, Betsy Cawn, 69, juggles a number of volunteer projects, including serving as the Outreach Coordinator of the multi-agency Lake County Clean Water Program.

“In Clear Lake, you have naturally high levels of phosphorus in the eroding soils, human-induced disturbances in the shore-proximate land areas, and massive amounts of deposited rich sediment in the ancient lake bed over the millenia,” says Cawn, with characteristic precision. “Yet, none of these disturbances have been mapped. The County and its responsible parties hardly do any monitoring. The whole system was — and is — jerry-rigged.”

The Agribusiness Connection

Most often, the main counterweight against greater regulation of water quality both in and nationally has been agribusiness. Farm drainwater caused selenium pollution of the Kesterson Wildlife Refuge in the San Joaquin Valley, which led to rapid die-off of migratory waterfowl, fish, insects, plants, and algae in the 1980s. The most severely polluted river of its size in the US has been (perhaps until recently) the New River, which drains from Baja California through California's Imperial Valley, carrying a stinking, swirling broth of more than a hundred toxic chemicals discharged by El Norte's agricultural run-off and pesticides, as well as maquiladoras on the Mexican side that discharge wastewater virtually absent of any oversight.

The state's agribusinesses, however, as with the agribusiness lobby on a national level, have waged a fierce battle to prevent greater regulation of water quality on farms. Whereas industry and sewers are regulated fairly strongly, agriculture is not.

Clear Lake's link to the state's largest agribusiness interests is not immediately clear, given that agriculture spans a relatively small portion of land within the lake basin. And most of the lake's “nutrient loading” clearly does not come from farms. But the lake is drained by Cache Creek, however, which is a tributary of the largest river in the state, the Sacramento River. And the Sacramento River watershed is home to an estimated 22% of California’s total farmland.

The Central Valley Water Board, which regulates water quality throughout the Central Valley, is also the regulatory body for Clear Lake. As with other agricultural entities in the Central Valley, the Water Board allows Lake County's agricultural operators to self-monitor their own run-off.

“We have waste discharge requirements for agriculture throughout the Central Valley, including Lake County, and grower coalitions have stepped up to pull together resources, monitor water quality, and draw from local expertise,” Central Valley Water Board Assistant Executive Officer Adam Laputz told the AVA. “Not just in Clear Lake, but throughout the valley, we're looking to get irrigated agriculture to get nutrient management plans in place to reduce the input of the nutrients.”

The county's official comments to the Central Valley Board on the occasion of the Board's mandatory five-year review of the TMDL plan points to the influence of agriculture within the county itself. In the past 15 years, Lake County's cultivated wine-grape acreage has soared to roughly 13,000 acres. And wine is the most politically powerful sub-set of agribusiness in California. In the review document, the Water Board devoted two paragraphs in a 38-page document to noting that conversion of several thousand acres of oak woodlands to corduroy-like rows of grapes, often on steep slopes, may contribute to the problem of “nutrient loading” in Clear Lake.

By contrast, the County devoted roughly half of its two-page comment letter to responding to these passing references. “We take exception of the portrayal of agricultural conversions on pages 9 and 10,” Lake County's comment letter author, Water Resources Engineer Thomas Smythe, wrote. “The vineyard conversion discussion is misleading and is likely to be cited in the future, even though there has been no documentation of the impact of agricultural conversions on erosion.”

While Lake County does have a grading ordinance that regulates vineyard development, this non-binding process applies only to conversions from existing agricultural lands to vineyards. The assertion that “there has been no documentation of the impact of agricultural conversions on erosion” is strange, given that Lake County was the location of one of the most infamous cases of vineyard-induced soil erosion: the Snows Lake Vineyard.

In 2001, a well-endowed Ojai, CA-based company bulldozed over 650 acres for vineyard development on Perini Hill outside of Lower Lake, including hundreds of native old-growth oaks, without any form of County review. As numerous residents noted at the time, the water of Seigler Creek ran red with the soil washed downstream from the erosion. The vineyard is called Snows Lake Vineyard.


Notably, this vineyard (one of the largest in Lake County) is now owned by E&J Gallo Corporation, the world's second wealthiest wine corporation by revenue. E&J Gallo is also historically the largest career donor of any individual company (according to the well-respected web site OpenSecrets) to the political campaigns of another Lake County grape grower: Rep. Mike Thompson, who represents the wine industry, Lake and Napa Counties, and parts of Sonoma, Solano, and Contra Costa Counties in the US House of Representatives. Thompson's laborers farm over 20 acres of sauvignon blanc in Big Valley (one of the main areas that washes sediment into Clear Lake), selling over 100 tons of grapes annually to multi-national corporation Brown-Forman's Bonterra Winery in Mendocino County.

Other vineyards have been controversial in Lake County. Burns Valley Creek traverses from its headwaters north of Highway 20 and down into Ogulin Canyon, where it acceps runoff from the 750-acre "Delta Breeze" vineyard, which has recently boasted a big "Re-Elect Jeff Smith" sign on the fence adjacent to its gate at the Highway 20 and 53 intersection (Jeff Smith is a Lake County Supervisor and owner of a local private water company). Design requirements for that vineyard operation were to include a handful of storage ponds, which were to be used for frost protection irrigation instead of drawing from the groundwater basin late in the rainy season. These never happened.

Other agricultural operators contribute to the problem. Upper Lake is the site of a 1,200-acre Army Corps of Engineers “reclamation project,” located south of the Nice-Lucerne cut-off, with this former wetlands now hosting hundreds of acres of rice fields that use lake water for flood irrigation. When the rice farms return the flood waters back into the lake, the lake receives the residues and applied contents of herbicides, fungicides, pesticides, and fertilizers. As studies have indicated, rice farming practices generate cyanobacteria, with four of the ten species being a strain called Gleotrichia, which is among those found commonly in Clear Lake.

As an example of how prevalent economic sectors often overlap in this region, one farmer flooding his reclaimed rice field with irrigation water is Mike Mountanos of the Mountanos Bros. coffee fortune, who has also invested his fortune in regional wine, real estate, and recreational ventures. He owns at least two vineyards in the Ukiah Valley. He also owns a ranch in the foothills of North Cow Mountain, west of Lakeport, that reportedly serves as a primary destination for recreational deer hunting trips involving other regional grape growers and other friends of his. The road Mountanos constructed to facilitate the deer hunts caused considerable erosion into Scott Creek. Mountanos also owns real estate throughout the Ukiah Valley, perhaps most visibly in the form of the gaudy apartment and office complex just south of Black Oak Coffee Roasters on North State St.

Lake County District Three Supervisor Denise Rushing explains that the county's defensiveness to the Central Valley Board comes from what she calls “a massive sensitivity to blaming the wine industry for the nutrient loading in the lake.”

“It's very easy for people to see algae in the lake, then look over and see all the vineyards and say, 'It's the wine industry,'” Rushing says. “And the wine industry, as with any agriculture, is going to be a contributor. But the wine industry also has some large-scale programs of education within their industry on how to do things sustainably. Meanwhile, there's lots of unregulated agriculture — pot farms — that are a big part of the problem.”


When I contacted the Lake County Farm Bureau to request comment for this story, Farm Bureau Director Allison Tucker directed me to contact a group called the Sacramento Valley Water Quality Coalition (SVWQC).

The Central Valley Water Board administers a program called the Irrigated Lands Regulatory Program (ILRP). It then allows the private, agribusiness-sponsored Water Quality Coalition to implement the program in Clear Lake. Notably, regulation via the private coalition makes individual farmers exempt from requirements to monitor pollution discharges. As a result, the Regional Board does not actually know where the pollutants are coming from, making it nearly impossible to identify how to reduce pollutants, according to critics. The Coalition also gathers very little data in Lake County. It maintains only one full monitoring station in all of Lake County, on Middle Creek upstream of Highway 20.

“There are two monitoring sites in Lake County,” Sacramento Valley Water Quality Coalition Director Bruce Houdesheldt told me via e-mail. “Middle Creek is the representative monitoring site. In the 13 Subwatersheds of the Sacramento Valley Water Quality Coalition, the representative site, is the site most frequently monitored (10-14 times a year) and is located where crops representative of the Subwatershed are located. McGaugh Slough is a management plan site and is monitored less frequently for specific parameters (e.g., dissolved oxygen)."

Critics point out that the lone site the Water Quality Coalition has selected, where "crops representative of the Subwatershed are located," actually has very little agriculture. The monitoring station may collect some information on run-off from walnut orchards and a few pears, but little else. No vineyards are located upstream.

The second monitoring station Houdesheldt mentioned, at McGaugh Slough, was originally the representative site when the TMDL program began in 2006. On its face, this location made far more sense: McGaugh Slough receives some of the run-off from agriculture in Big Valley, including lots of vineyards. It is unclear why the Water Quality Coalition opted to stop conducting full monitoring there. However, it is known that elevated levels of ecoli were detected in three of the four so-called “monitoring events” the Water Quality Coalition conducted there. If ecoli had been detected in the next monitoring event, it would have led to the EPA's listing McGaugh Slough as an “impaired” water body under Section 303D of the Clean Water Act, making it subject to far more monitoring and regulation, including its own TMDL.

Instead, the Water Quality Coalition created a new primary monitoring station and stopped testing for coli in McGaugh Slough.

Notably, the Sacramento Valley Water Coalition is an official project of an organization called the Northern California Water Association, which is one of Sacramento Valley agribusiness' primary lobbying organizations. With an office on the Capitol Mall in Sacramento, this quasi-regulatory agency has lobbied strongly in the California State Legislature on behalf of the Sites Reservoir, which I have discussed in past articles. In one of its brochures, the NCWA states that the facility is "being designed to to provide more reliable water supplies for cities, farms, birds, fish and recreation."

Meanwhile, the other entities responsible for reducing nutrients into TMDL also appear to be conducting little monitoring (a subject that merits another article to explore fully). "It was clear after reading the five-year update to the TMDL that no monitoring was being done by the county to speak of," Sarah Ryan of the Big Valley Band of Pomo Indians Environmental Department said. "That's really notable when we have the potential for toxin levels really impacting recreation and municipal uses of the water."

According to Denise Rushing, who is Lake County's most left-leaning supervisor, the lack of monitoring is strictly due to a lack of funding. “I would give Lake County an 'A' for effort and a 'D' for effectiveness when it comes to dealing with nutrient loading,” she said. “We don't have very much money, so a lot of the money we do get we devote to symptoms of the problem, as opposed to root causes.”

As Betsy Cawn points out, most of the lands responsible for nutrient pollution of Clear Lake are outside of the County's control — national forest, Cow Mountain, etc. However, the County could be doing far more to coordinate the various parties, she points out. In 2004, California State Senate Bill 1136 authorized "watershed protection districts" within various counties to carry out new mandates to safeguard their own water quality. The Lake County Watershed Protection District, for instance, has the authority to obtain federal and state grants and raise taxes, which could, for instance, be used to set up monitoring stations around the Lake. The District is governed by the Board of Supervisors, acting as the Board of Directors.

It does not appear that the Watershed Protection District has sought to improve water quality monitoring in Clear Lake, let alone coordinated activities involving the US Forest Service, Bureau of Land Management, and other entities responsible for Clear Lake's phosphorus problem.

Middle Creek Marsh Restoration

Meanwhile, one of the most positive efforts to improve the health of the lake that has emerged in recent years is an Army Corps of Engineers-backed wetlands restoration program on the Middle Creek Marsh, which the Corps originally filled in to create agricultural land near Nice and Upper Lake in the 1920s and 1930s. The Corps, the State of California, and the County of Lake have been collaborating to purchase land from willing sellers in the area for several years, so as to pave the way for the restoration project — the most ambitious in Lake County's history.

The Project area was “reclaimed” between 1900 and 1940 by constructing levees, creating Rodman Slough, and "reclaiming" approximately 1,200 acres of lake bottom and shoreline wetlands for agricultural purposes. In 1958, the Corps of Engineers added to the levee system, reclaiming an additional 200 acres of shoreline wetlands. These projects resulted in the physical isolation of over 1,650 acres of wetland and floodplain from the largest tributaries of Clear Lake. If the wetlands were restored, it would remove up to 30 percent of the phosphorus that currently washes into the Lake.

“I feel it's one of the most important things we can do for Lake County,” Supervisor Rushing says. “Actually, it's a tragedy that those levees got built in the first place.”

Numerous things stand in the way of the project's successful implementation. PG&E has determined it would have to move several transmission towers, and that it's the county's responsibility to carry out this process, at an estimated cost of $5 million. Meanwhile, the rice growers currently using lake water for flood irrigation in the reclaimed lands have been unwilling to sell their properties.

Notably, when the Army Corps of Engineers constructed the levees, they used soil from a hill called Eastside Peak as fill. Following the Bloody Island Massacre of 1851, the surviving Pomo people took their dead up to Eastside Peak to bury them. In a sense, then, the wetlands that need to be restored if Clear Lake is ever to return to health are filled in with the remains of massacre victims.

Contact Will Parrish at

[Update, 11/10/2014: An earlier version of this article incorrectly said Lake County's task force monitors the lake for cyanotoxins. The monitoring is conducted by the Big Valley and Elem bands of Pomo Indians. Also, the article had failed to mention that the monitoring focused on cyanotoxins.]



  1. Jim Armstrong November 7, 2014

    The high phosphorus area in the top left of the photograph that Will identifies as Lake Pillsbury is actually Tule Lake, a seasonal body of water that lies along the south side of Highway 20 between Upper Lake and Witter Springs.

    • AVA News Service November 7, 2014

      Thanks, Jim. You are correct about Tule Lake, but wrong about an error on the author’s part.

      The image Mr Parrish originally suggested included Lake Pillsbury. We ended up choosing a zoomed image of Clear Lake, for clarity and detail.

      To help clear the misunderstanding, we’ve appended the unzoomed image to the end of the article.

  2. wparrish November 7, 2014

    True… actually, Pillsbury is in the map I referenced, in the upper left portion, but the version published here is a zoomed-in version that focuses more clearly on Clear Lake but excludes Pillsbury.

  3. Jim Armstrong November 7, 2014

    Thanks to both of you. Good article.

  4. John Parker, Ph.D. November 10, 2014

    Great job Will. Thanks for the in-depth information. Tule Lake is also part of the problem. Once filled with tule (as its name implies), it is now in rice production and the filtering of storm water run-off that the tules once provided is no longer happening along this stretch of Scotts Creek.

Leave a Reply

Your email address will not be published. Required fields are marked *