President’s Message: A New Age Begins to Dawn in the Deschutes Basin

By Greg McMillan

Our favorite river, and its tributaries like the Crooked River, have suffered abuses and hard times for many decades.  The pressures on water quality, availability, and the biology they support have increased.  There are now three aquatic species listed as threatened or endangered under the Endangered Species Act in the Deschutes Basin.  There are species that have already been extirpated from their historic ranges within the Basin.

Picture 040

Photo credit Greg McMillan

In this post is news of another insult.  Chlorpyrifos pesticide has been detected in the Deschutes River in levels that exceed what the Environmental Protection Agency has set as guidelines to protect aquatic life.

But there is more hope for the Deschutes Basin and its aquatic resources today than in a very long time.  It is said (perhaps truthfully so) that the Chinese character for crisis is a combination of the characters for danger and opportunity.  And so it is with the Deschutes River and its tributaries.  We are on the verge of several dangerous opportunities.  It’s taken years of hard work to arrive at this new threshold.

The multi-year water quality report recently released by Portland General Electric and the Confederated Tribes of the Warm Springs Reservation confirms what we here at the DRA have known since 2014.  Having consensus on the scientific issues gives the parties in our lawsuit a common path forward to resolve the Round Butte Dam Selective Water Withdrawal Tower related water quality problems.  It will take time and hard work, but finding consensus is a most important first step.

The other large water problem in Central Oregon is related to water allocation for irrigation.  That issue first came to a head with the listing of the Oregon Spotted Frog (OSF) population as threatened under the Endangered Species Act in 2016.

This status of the OSF is due to de-watering of its native habitat in the reaches of the Upper Deschutes River below Wickiup Dam during fall and winter months.  Water is held back for storage for irrigation purposes during those months, leaving the back-channels and marsh habitat of the frog below the dam dry.

The irrigators and the City of Prineville have applied to the U.S Fish and Wildlife Service for an Incidental Take Permit to allow for the loss of Spotted Frogs, as well as bull trout and steelhead due to water allocation issues.  The permit requires a Habitat Conservation Plan (HCP) to off-set any losses due to the water withdrawals by the irrigators or City of Prineville.

As you read this, many organizations, agencies and individuals will be submitting comments on a draft HCP.  DRA is one of the organizations submitting comments.  It’s our view that the HCP is inadequate to provide adequate protection for the target species.  We will be participating in the HCP process and advocating for changes in water allocation.

You can read our comments here.

As we move forward this is an opportunity to re-think how water is used in the Deschutes Basin.  The plan, once approved, will be binding for thirty-years.

We will be working with other groups and our Oregon legislators to enact a ban on the insecticide chlorpyrifos.

These crises are indeed dangerous opportunities.  There is no better time to affect how the future of the Deschutes River and its tributaries will look for the next decades to come.  We have to get it right for the river and for the next generations.  There will be no other time like right now, no other opportunities like those before us to protect our river.

Please help us in this time of need and opportunity.  Your donations will help us advocate for the changes that need to be made. There are issues that need to be resolved and with a sense of great urgency. You can donate online here.

DRA Legal Update

By Dan Galpern

To restore and protect the Deschutes River, time and again the DRA has turned to bedrock federal law—including the Clean Water Act, which commits the nation to “restore and maintain the chemical, physical and biological integrity” of U.S. waters. It is therefore important, at the outset of this brief update, to recognize that the CWA expressly enables citizens, including public interest groups, to enforce the law when government agencies fail to act.

Accordingly, on August 12, 2016, on behalf of its supporters and in the public interest, DRA filed suit in federal court to uphold critical CWA water quality standards that DRA alleged were being violated by PGE’s operation of the Pelton Round Butte Hydroelectric Project and, in particular, operation of the Project’s Selective Water Withdrawal tower.

Crooked River photo 1

Photo by Rick Hafele

Section 401 of the Clean Water Act is central to DRA’s case. It requires applicants for federal licenses (such as the FERC license for the Pelton Round Butte Project) to provide the licensing agency (here, FERC) with a state certification (the CWA Cert) that project discharges will comply with minimum state water quality standards. Those standards are written to support specified uses, including fishing and recreation. DRA’s lawsuit was based on what it alleged to be documented exceedances of standards for temperature, dissolved oxygen, and pH. Arguments in court centered on whether such discharges violated the Project’s CWA Cert. DRA’s next step after obtaining such a ruling from the court would have been to seek an order from the court prohibiting continued operation in violation of such standards. But the lower court rejected DRA’s arguments, and DRA appealed that ruling.

A critical interim legal development merits explanation. Seven weeks after DRA’s initial filing, PGE brought a motion to dismiss. Its grounds: that the Court retained no authority to decide the case. In short, the company argued that the CWA enabled the state to include conditions in a CWA Cert but that, once done, only the federal licensing authority—here, the Federal Energy Regulatory Commission—could enforce those conditions.  Not EPA, not states, and not citizens.

Briefing and argument ensued, and DRA finally prevailed in March 2017. In a published decision, the Court determined that “citizens may sue both to require a facility to obtain certification and to enforce conditions in an existing certificate.” [Emphasis added.] The Court declared its reading of the citizen suit provision to be “the only construction that is consistent with the text of the statute and the purpose and policy of the CWA, while also upholding a state’s authority to enforce its own water quality standards.” Deschutes River Alliance v. Portland General Electric Company, 249 F.Supp.3d 1182, 1194.

PGE then appealed that decision to the 9th Circuit Court of Appeals, and DRA opposed that appeal. In August 2017 the 9th Circuit summarily denied PGE’s appeal. Accordingly, the district court’s determination that citizens (and states) have the right to enforce terms and conditions of §401 CWA Certs remains undisturbed. To date.

A series of proceedings, including briefings and hearings, subsequently ensued. In order: (1) The Confederated Tribes of the Warm Springs Reservation, as co-owner of the Project, sought to dismiss the case on the ground that it was a necessary party to it and yet immune from federal suit. But, after briefing, the court determined that while the Tribe was a necessary party, it was not immune, and so the Tribe was joined in the case as a defendant. (2) All parties then filed for summary judgment on the merits, and argument was held. (3) The district court rejected DRA’s motion for summary judgment and granted summary judgment to PGE and the Tribe, thus dismissing the case.

In its August 3, 2018 opinion and order, the court rejected DRA’s strict interpretation of the law, namely, that every exceedance of a water quality standard constitutes a violation of the CWA Cert and its associated water quality monitoring and management plans. The court agreed that, based on the company’s analysis and modeling, the CWA Cert had, in fact, anticipated that the Project would conform to state water quality standards. Nonetheless, the Court stressed that while “this calculation may have been wrong does not necessarily mean that Defendants are violating their Certification.” Deschutes River Alliance v. Portland General Electric, et al., 331 F. Supp. 3d 1187, 1209 (Aug. 3, 2018) (emphasis in original).[1]

DRA respectfully believes that the district court erred in several critical respects, including its deference to DEQ as to applicable standards and the compliance record and the court’s disinclination to read CWA Cert water quality conditions as strict limitations. Accordingly, on October 17, 2018, DRA appealed the Court’s final order and opinion to the 9th Circuit Court of Appeals. Two weeks later, PGE and the Tribe each filed notices of cross-appeal, albeit on a protective basis—that is, “only in the event that the court of appeals reverses the judgment in defendant’s favor on the merits.” Accordingly, through these conditional appeals, the 9th Circuit could be required to review the district court’s rejections of the earlier PGE and Tribe motions, that is, those seeking dismissal for failure to join a necessary party and seeking to dismiss for lack of jurisdiction.

In the meantime, however, PGE and the Tribe released their long-awaited contracted study of Project impacts on critical elements of Deschutes River water quality. As DRA previously reported in these pages, the DRA Science Team closely reviewed the report after its publication, and DRA deemed substantial portions of it to be sound and significant. Thus, a meeting of the minds now may be more feasible than before. In part for this reason, the parties have delayed briefing at the 9th Circuit to allow for settlement talks. At this juncture, we cannot foretell whether settlement will be achieved, but DRA is determined fully to test these waters to discern if they harbor a more direct course to restoration of the ecological integrity of the lower River. Crucial determinations in this regard may materialize in the next several months.

Finally, we must turn to a regrettably relevant aspect of the Trump Administration’s frantic drive to eliminate environmental protections by executive order. In late August 2019, Andrew Wheeler, Administrator of the Environmental Protection Agency­—and former counsel for the now-bankrupt coal company Murray Energy—published a draft rule that would eviscerate Section 401 of the CWA if enacted. Among other things, the rule would specify that it is the federal licensing agency alone that can enforce CWA Cert terms and conditions. DRA’s comments to EPA, filed on October 21, 2019, expose the agency’s attempted regulatory legerdemain as contrary to the specific terms of the CWA, and warns that the agency’s “patent attempt to displace citizen and state authority to enforce §401 terms and conditions will not stand.”  See here.

Though we scarcely knew it at the time, we were in good company. Over 200 other substantive comments were filed on the final day EPA allowed comment—even though the draft EPA rule, on its face, appeared highly and merely technical. By my office’s analysis, the overwhelming majority of these (~78%) were squarely against the proposed rule. We are now reviewing the major comments, including those by industry, to discern prospects for legal challenge — if and when the EPA rule becomes final.

Former Supreme Court Justice William Brennan once stated emphatically that “enforcement of the law is what really counts.” DRA is mostly doing that, but at times we also need to defend the law itself.


The writer serves, along with Doug Quirke of Oregon Clean Water Action Project, as outside counsel to DRA.

[1] In its opinion the district court also observed that “[t]o the extent it has turned out not to be the case that operation of the SWW pursuant to the management plans can result in compliance with state water quality standards, the appropriate challenge would be to DEQ’s approval of the Certification itself—not to Defendants’ operation of the Project. Id. at 1201. The Court also cited to DEQ’s publicly stated intention to modify the CWA Cert in a process that will include a notice and public comment period. Id. at 1197. DRA intends to fully participate, assuming that DEQ follows through.

What Can We Do to Help Lake Billy Chinook?

In spite of years of pollution and regulatory inaction, Lake Billy Chinook is not doomed to its current harmful algal bloom (HAB) fate. The current oversight system cannot bring about this needed progress and must be changed. That change starts with increasing monitoring and sampling efforts at Lake Billy Chinook, which can begin describing current conditions more precisely and lead to better response actions. To stem HABs quickly, nutrient pollution from the Crooked River must be addressed. By both targeting the source of pollution and through mitigation efforts, Lake Billy Chinook and the whole Deschutes Basin can begin the healing process. But this cannot happen without your help. With a strong coalition, a unified voice, and constant advocacy, lawmakers and regulators will have to seriously consider and start responding to Lake Billy Chinook’s HABs issue. Support and join DRA in our advocacy and have your voice heard by regulators and your elected officials about this vital issue.

LBC algae 1

Current Gaps

As discussed in our two previous posts, the HAB situation at Lake Billy Chinook is complicated, but not unfixable. The increasingly common HABs result from a combination of factors – high nutrient pollution levels from fertilizer and fecal waste chief among them. These blooms harm not only the reservoir and the species that call it home but also strain the local economy and pass the water quality issues onto the lower Deschutes River.

Despite the consistency of HABs and the contribution from nutrient pollution, very little responsive action has taken place. While the Oregon Health Authority issues health advisories for the reservoir, very little monitoring and even less sampling takes place. Monitoring is sporadic at best, and sampling occurs even less frequently. The result creates Lake Billy Chinook-sized blind spots about HAB sizes, severity, and longevity, and the conditions leading up to the bloom. Very little effort has gone into identifying and addressing the specific causes of harmful algae blooms. Over nearly two decades of poor water quality, the State of Oregon has not made any significant progress in bettering LBC’s water quality. Likewise, little has been done to stem nutrient pollution’s contributions, either at the source or through mitigating efforts. Without even the most basic steps, a successful recovery process cannot begin. In the meantime, the biggest symptom – HABs – are left unchecked and will continue to bear their ugly heads.

LBC 7What to Do

Two closely connected initial steps are needed before recovery can begin in earnest – increased monitoring and sampling at Lake Billy Chinook and its tributaries as well as nutrient pollution response actions. Monitoring and sampling must occur at more locations and much more frequently. The information that this increase will immediately provide about LBC and its HABs will not only allow for better public advisories for on-reservoir recreation but will also better inform lower Deschutes River users. Crucially, the information can also describe conditions leading to HAB occurrences, allowing for better prediction. Monitoring tributaries, like the Crooked River, more closely will better identify contributing factors and precisely target future responsive actions in the areas of most need. Expanded monitoring and sampling will bring both immediate and future benefits to Lake Billy Chinook and all that enjoy and rely on the reservoir.

While expanding our understanding of Lake Billy Chinook’s HAB situation, nutrient pollution must also be addressed. Heavy nutrient pollution from the Crooked River feeds HABs in LBC. This nutrient pollution comes from agricultural runoff resulting from the large amount of farming and grazing in the area. Fertilizer and animal waste – high in nitrates and phosphates – are swept up by overwatering practices and are discharged directly into the Crooked River. This agricultural runoff makes up a considerable portion of LBC’s nutrient load. By supporting and implementing on-farm water efficiencies, less nutrient-laden water would return to the Crooked River. It would have the added benefit of reducing water withdrawals from the river, which would improve water quality. On similar lines, supporting and reworking fertilizer application and animal waste disposal would also help to reduce nutrient pollution.

Moving away from direct sources, increasing riparian buffers along the Crooked River would help lessen nutrient pollution. These vegetative intermediaries act as a buffer by soaking up and slowing runoff and holding onto the nutrients before passing on the filtered water into the adjacent waterway. Implementing land use rules, especially in heavily agricultural areas, that require these riparian buffers would help stem direct runoff into the river. It could have the added benefit of providing habitat for threatened species and a cooling effect on both the overly warm Crooked River and in Lake Billy Chinook. These two steps, addressing the sources and mitigating the impact of agricultural runoff, would benefit not only Lake Billy Chinook but the Crooked and the lower Deschutes rivers too. Combined with more precise information from increased monitoring and sampling, regulators and lawmakers can begin to successfully address this basin-wide issue.


Harmful algae in Lake Billy Chinook is not an insolvable problem. With monitoring, data, and fact-based advocacy, we can make a difference. We can take steps to mitigate HAB-causing nutrient pollution right now by creating and expanding riparian buffers in the Crooked River. But advocacy must target the root causes – agricultural runoff and overwatering – to be successful. Additionally, the true extent and specifics of nutrient pollution in Lake Billy Chinook cannot be understood without more consistent monitoring and sampling. Find your local representatives, call or write them, and raise the issue of HABs in Lake Billy Chinook whenever you can. Join the DRA in bringing about solutions that will rehabilitate Lake Billy Chinook and our local ecology and economy for years to come and for future generations to enjoy.

Accomplishments from 2019

Legal and advocacy

Our Clean Water Act lawsuit against Portland General Electric (PGE) and the Confederated Tribes of the Warm Springs Reservation of Oregon (CTWSRO) was appealed by DRA to the Ninth Circuit Court of Appeals. We will continue this important legal battle until appropriate and necessary improvements in water quality below the Pelton-Round Butte Hydroelectric Complex are made.

DRA believes that the reintroduction of salmon and steelhead above the dams would have a greater chance of success if the fish were trucked around not only the dams (as they presently are) but around Lake Billy Chinook as well. This would allow for changes to the mix and timing of water releases that might substantially restore water quality in the lower Deschutes River. DRA will continue advocating for this change to the fish reintroduction efforts. Read more here.

DRA submitted comments to the EPA concerning its Harmful Algae Bloom and Hypoxia Policy development, raising concerns and suggesting protections around Lake Billy Chinook and Central Oregon communities. DRA has also been an active participant in the Oregon Legislature’s Harmful Algae Bloom Workgroup. Read the comments here.

DRA advocated for an adequately protective Habitat Conservation Plan for the steelhead and bull trout, Sockeye and Chinook salmon, and Oregon Spotted Frogs. The guidelines of the HCP must provide for the needs of each ESA-listed species as specified in their specific Biological Opinions. Read our comments here.

DRA opposed a Trump-EPA draft rule that would virtually eliminate the utility of a key Clean Water Act authority.  Clean Water Act Section 401 requires states to impose conditions on federally-licensed projects that can impact water quality, including hydropower projects. The proposed rule would eliminate the ability of citizens and states to enforce those Clean Water Act conditions. Read our comments here.


In May, DRA released our 2018 water quality report – our fifth annual report. Results from 2018 again showed numerous exceedances of Oregon’s water quality standards in the lower Deschutes River. In June, PGE and CTWSRO released their own study that confirms DRA findings and provides evidence that operations of the Selective Water Withdrawal Tower must change quickly to prevent further ecological deterioration in the lower Deschutes River. If these changes are not made in a timely and meaningful manner, then the fish, wildlife and people who count on this formerly healthy national treasure and internationally famous fly-fishing river will continue to suffer. Read our analysis here.

LDR boat 3

DRA released its “Water Quality and Land Use in the Crooked River Basin” report in February. This report will be the first in a series of meaningful steps to address nitrogen pollution in the Crooked and lower Deschutes rivers. Since Tower installation more warm and polluted water from the Crooked River flows into the lower Deschutes, degrading water quality, disrupting critical fish habitat and fundamentally changing the ecology of the river.

Our first Benthic Report was released in October and documents three major changes in aquatic insects. First, there has been a significant increase in pollution-tolerant worms and snails with a parallel decline in pollution-intolerant mayflies and stoneflies. Second, there has been a decline in the general abundance of adult aquatic insects, which affects food availability for fish as well as many bird species along the river. And third, there has been a dramatic increase in worm and snail species that serve as the intermediate hosts of serious fish parasites and as indicators of more polluted water. These changes are the direct result of a decline in water quality.

In 2020 we will be releasing a water quality report for Lake Billy Chinook – the first DRA report to focus on the reservoir. The report will demonstrate that the surface layer of the reservoir is toxic for juvenile fish and is impeding reintroduction efforts. Particularly alarming are the high pH levels in the surface layer.

DRA staff have submitted a research poster to the Oregon Chapter of the American Fisheries Society and hope to present it at the Oregon AFS Conference in March 2020. The poster focuses on the impacts that the Crooked River has on water quality and the change to pollution tolerant aquatic life forms in the lower Deschutes River.

We launched a new, updated Deschutes Hatch Survey app in cooperation with Trout Unlimited – a record number 170 surveys were submitted by qualified observers in 2019. The full report will be released later this year.


In February, we again threw one heck of a party at our third annual Gathering and Auction. It was a fun filled event to highlight our community and support the work to preserve and protect the river. We will be doing it again on February 8, 2020 – join us!

In September, we hosted our first annual BBQ in Maupin as a way to say thank you to the community for its strong support. It was a fun-filled afternoon with live music, beer and food. We can’t wait to do it again next year!

DRA supporters continued backing our Maupin community through river clean ups and by continued care for our adopted stretch of highway at a gateway to Maupin.

We experienced some transitions as we said goodbye to some staff and welcomed others. We wished Jonah Stanford well in his new endeavors. We also welcomed our new Executive Director, Sarah Cloud, to the DRA team. We are excited for new opportunities, continued advocacy and research, and whatever else the future holds.

Why Have Harmful Algal Blooms on Lake Billy Chinook Seemingly Increased?

Across the world, reported numbers of toxin-producing harmful algal blooms (HABs) in freshwater bodies have spiked. Oregon does not escape this fate. Lake Billy Chinook has seen HABs each of the last five summers – an alarming development. These HABs threaten water quality, strain local economies, and affect the health of people, fish and wildlife, and whole ecosystems. Though many point to climate change as the spike’s main cause, that explanation fails to look at the whole picture. A better explanation for the spike is human activities, especially those that pollute water, impair water quality, and provide optimal conditions for HABs to flourish in. At Lake Billy Chinook, the major contributors are nutrient pollution from agricultural runoff, the loss of riparian habitat along its tributaries, and impounded, stagnant waters. Looking at all of these additional pressures, the increasing frequency of HABs at Lake Billy Chinook is a foreseeable outcome.

How do HABs form in the first place?

Algae flourish in warm, sunny, stagnant waters with high nutrient contents. Warm and stagnant waters allow algae to occupy the surface of the water without being disturbed and sunlight allows photosynthesis and growth. Unnatural infusions of nutrients give algae the building blocks they need to continue to grow in dense concentrations. These conditions readily result in large HABs.

Nutrient polluted freshwater systems impair water quality to algae’s benefit. Some of the largest contributors to HAB-causing water quality impairment are nutrient pollution from agricultural runoff and forestry practices, removing riparian habitat which filters runoff and provides shade, and increasing temperature through water withdrawals and stagnation. The HABs resulting from these activities point to a larger issue – freshwater systems are overtaxed by nutrient and temperature pollution and can no longer function properly.

Climate change is responsible for some water warming and providing favorable weather conditions for algae. However, if climate change was the main contributor, similarly situated freshwater bodies would experience HABs at similar rate – which they are not. Human activities that pollute and impair water quality provide a better explanation for this difference in HAB occurrence rates.

Why is Lake Billy Chinook seeing so many HABs?

Lake Billy Chinook is at the forefront of the HAB spike in Oregon. It owes this dubious distinction to the excellent conditions it provides for algae to thrive in. Nutrient pollution is high, surface water temperatures are above healthy levels, and the water is largely stagnant. With these conditions, the significant uptick of HABs at Lake Billy Chinook is not too surprising.

But how did conditions at Lake Billy Chinook get this way? Human activities throughout the Deschutes Basin are the main contributor. Agricultural runoff transported by the Crooked and middle Deschutes rivers, lost filtration and shade once provided by riparian vegetation along the tributaries, water withdrawals, and impoundment operations all impair Lake Billy Chinook’s water quality and offer optimal conditions for HABs.

The water quality situation at Lake Billy Chinook is unique in that it is largely at the mercy of its three tributary rivers for its own water quality – the Metolius, Deschutes, and Crooked rivers. Lake Billy Chinook’s nutrient pollution problem comes largely from one source – the Crooked River. Runoff from both animal feed operations and farms, which use 25% more fertilizer compared to 55 years ago, enter directly into the Crooked River. That runoff is no longer filtered by riparian vegetation. The Crooked River’s nutrient infusions, which account for 86% of Lake Billy Chinook’s dissolved nitrates, feed algae and potential blooms.

Lake Billy Chinook’s high temperature comes from many sources. Climate change, however, is not a major contributor. Over the last 20 years, surface water temperatures at Lake Billy Chinook have not increased much. On the other hand, many temperature-raising factors have stayed constant during that same period. Both the Deschutes and Crooked rivers’ temperatures are, and have been, well above the protective criteria level set by the State for the Deschutes Basin. Water withdrawals continue to reduce the amount of water in the Deschutes and Crooked rivers, allowing them to warm more quickly. Finally, impounding water both increases the exposure time of water to more solar radiation, which increases water temperature and stimulates algal growth. These conditions have persisted during the last 20 years and explain Lake Billy Chinook’s high temperatures better than climate change.


Freshwater bodies are in a constant, delicate balance with countless factors contributing to their health and status. Lake Billy Chinook provides a clear example of how the human activities are the major contributing factor to the HAB spike, both locally and worldwide. Climate change alone cannot explain this spike. Nutrient pollution and temperature-increasing human activities provide a clearer explanation. Lake Billy Chinook’s current water quality conditions provide a nutrient-rich, warm, and stable environment for algae to thrive year after year. If these conditions continue, HABs will continue to occur in Lake Billy Chinook.