Judge Gets Good News Update In Biop Lawsuit
 46,000 Fish In One Day: Fall Chinook Run On Way To New Record
 Lower Granite Fall Chinook Numbers Headed For New High
 Recent Ocean Surveys Support Regime Shift In Eastern Pacific
 Hatchery Fish May Not Be Good Stand-Ins For Wild Fish
 Study Says Methow Irrigation Canals Recharge River Flows
 Crapo Calls For Mediation In Idaho Water Dispute
 Grant PUD Meets Fish Survival Goals
 JUDGE GETS GOOD NEWS UPDATE IN BIOP LAWSUIT
Federal judge James Redden got a crash course in salmon recovery last week when federal agencies gave him their first quarterly report on progress towards making the hydro BiOp conform to what he considers requirements of the Endangered Species Act. In May, the judge gave federal agencies a year to fix the BiOp and report every 90 days on progress.
The report included federal action agencies' "2003 check-in" document, a requirement from the old BiOp to gage progress of its implementation. The check-in positively gushed over recent salmon returns, noting that seven of the eight ESUs [Evolutionarily Significant Units] jeopardized by hydro operations "are showing significant improvement.
"Runs of most listed fish were several times greater than their 10-year averages during the first two years after the 2000 BiOp was issued," says the report.
Judge Redden had made earlier remarks that seemed out of touch with recent record fish runs. In May, he said he hoped the endangered fish issue could be settled before "someone catches the last one."
The check-in also pointed out that the federal government has spent nearly $2 billion on West Coast salmon recovery efforts in the past three years and was expecting to spend more than $700 million in 2004.
Though subbasin planning efforts are taking longer than expected, the report said hundreds of ongoing actions are being funded for habitat improvement and hatchery programs and future actions are being prioritized to focus on helping anadromous stocks.
The report also included long tables of recent NOAA Fisheries updates of their arcane mathematical analyses that estimated the rate of improvement needed by various ESUs to have less than a 5 percent chance of going extinct over the next 100 years.
The latest NOAA analysis didn't boost rates of improvement much from earlier estimates in the BiOp, though populations of some ESUs were now seen to be trending upward, especially when data before 1990 was excluded.
However, the latest analysis didn't include the excellent run numbers from 2002 and this year, which the feds have promised to include in their next analysis ready by next spring, as part of an overall update of the status of the listed stocks in the basin, which will be used to "refresh" the jeopardy analysis.
The NOAA analysis shows only the lower Columbia chum spawning aggregation may not need additional survival improvements. Steelhead in both the upper Columbia and Snake would need the most help. "Under all assumptions" and for all its spawning components, the survival rate of upper Columbia steelhead would have to increase by seven-fold to meet federal criteria, which includes "whether or not there would be at least a 50 percent probability of the 8-year geometric mean natural spawners being equal to, or greater than, interim recovery abundance levels in 48 and 100 years as a primary "metric indicative of recovery."
But some of those criteria have been strongly criticized by some groups as "misleading and absurd standards." That was how the Columbia-Snake Irrigators Association and Eastern Oregon Irrigators Association characterized the current BiOp when they announced earlier this week they were filing a lawsuit against NOAA Fisheries and the 2000 BiOp, which they say is based on an "Orwellian re-definition of the 'risk of extinction."
They say the federal fisheries agency has found dam operators single-handedly responsible for guaranteeing salmon recovery, while discounting the "enormous" natural mortality that occurs to fish in rivers with and without dams.
The irrigator groups' spokesman Darryll Olsen said the Bush Administration "needs to come to reality on salmon."
Pointing to the large returns in recent years of both hatchery and wild fish in the Columbia Basin, Olsen said he hoped his lawsuit would have some effect on NOAA Fisheries as it re-writes the hydro BiOp during the remand process.
However, judging from what the feds told the court last week, it seems that a prospective new BiOp may take a bigger bite out of the region than before.
Judge Redden had ruled that the BiOp was too vague about whether salmon mitigation actions outside the hydro system "were reasonably certain to occur." To satisfy his concerns, NOAA now says it will expand the definition of the "action area" in question to include not only areas that are directly and indirectly affected by the federal hydro system, but "also any watersheds in which off-site mitigation activities required by the RPA [Reasonable, Prudent Alternative] may occur." The agency said the change would mean that the new action area "will cover, most if not all, of the freshwater habitat of the affected ESUs discussed in the 2000 RPA."
But James Buchal, the irrigator associations' attorney, was not encouraged by the direction of the re-write. "The defendant's latest status report demonstrates that the Bush Administration intends to hold dam operators single-handedly responsible for offsetting effects in an 'action area' that embraces much of the Pacific Northwest," Buchal said, "through thousands of pages of planning documents that will require an ever-growing bureaucracy of Soviet proportions to implement. This effort is destined to collapse of its own weight."
The first quarterly report also said the "reasonable certainty" test is a not a one-way street, but "must be equally applied to both future potential beneficial and future harmful actions." The agency said that means it must re-evaluate the way future harmful effects of state and private activities were addressed in the old BiOp "to ensure that only those future harmful effects which can meet the "reasonable certainty" test are considered.
To some, that language means more scrutiny over future harvests, since it's likely that harvest rates will be increased as fish runs improve. The past few years, state and tribal fish managers, with federal approval, have already bumped up catches as spring and fall chinook runs have been setting records. -Bill Rudolph
 46,000 FISH IN ONE DAY: FALL CHINOOK RUN ON WAY TO NEW RECORD
After several days of spectacular returns plugging the fish ladders at Bonneville Dam, Columbia Basin harvest managers decided to revise their estimate of the fall chinook run. On Sept. 17 the managers added another 200,000 fish to their original prediction. The 2003 fall run is now estimated at 813,000 fish to the river mouth.
On Sept. 11, nearly 46,000 fish were counted at Bonneville, with only a few hundred less tallied the following day. On Sept. 13, the count was still high, at 39,642 fish. The old one-day record of 39,376, set in 1987, was topped three days in a row.
September crowd at Bonneville Dam.
The monster run took everyone by surprise, since part of it, the two-ocean component that had spent two years at sea, is made up of fish that migrated during the drought year of 2001, when no water was spilled for salmon passage at federal dams for weeks at a time. Preliminary results from two weeks of sampling scales of returning fish showed only about 5 percent of the run was made up of 2001 outmigrants, but analysts cautioned that the sample rate was small--less than 300 fish out of nearly a quarter-million that passed the dam during those two weeks. Last year, the sampling effort found that about one-quarter of the run was made up of two-ocean fish (from brood year 2000), with about 40 percent three-ocean fish. The age composition has fluctuated quite a bit over the years. The average 2-ocean component of upriver brights from 1983 to 1987 didn't even amount to 15 percent of the run, which included the 811,000-fish return (counted to river mouth) of 1987, according to earlier BPA-funded analyses.
Harvest managers say that 515,000 bright falls, both upriver and mid-river varieties, are now expected to enter the river. The update adds 109,000 more fish to the upriver estimate of fish bound for the Hanford Reach and another 80,000 hatchery fish (tules) headed for Bonneville Pool to the original 102,000-fish estimate.
That translates into 426,000 brights and 167,000 tules that are now expected to be counted at Bonneville Dam.
By Sept. 29, the Bonneville fall chinook count added up to 587,000 fish, which already tops the huge returns from the past two years--both record years that topped 1987's 337,00-fish fall return, the dam's previous personal best.
Managers agreed to boost harvest in both non-Indian and tribal fisheries. Indian fishermen had caught more than 55,000 fall chinook by Sept. 12, while the non-Indian catch was projected to add up to 102,900 fish, with sporties expected to make off with about 47,000 fall chinook by the time it's all over. -B.R.
 LOWER GRANITE FALL CHINOOK NUMBERS HEADED FOR NEW HIGH
The huge wave of fall chinook that has inundated Bonneville Dam the past few weeks finally reached the lower Snake. Although it's a tiny ripple by the time the Snake run peels off for Idaho, it may set a new record.
More than 18,000 fall fish have been counted at Ice Harbor Dam, the lowest counting station on the Snake, while 9,160 have been tallied coming out the upper end of the lower Snake corridor, headed for spawning grounds below Hells Canyon. Aided by a supplementation effort the past few years, that's considerably above the 10-year average of about 1,400 fish.
By this time last year, about 9,000 hatchery and wild fall chinook had been counted passing the dam, but several thousand fewer fish had entered the Snake by now.
Fish agencies still haven't released their estimates of wild returns for 2001 and 2002. It's a complicated chore, since many hatchery fish masquerade as wild ones because their adipose fins were not clipped to distinguish them from the ESA-listed wild run. It has created an actuarial quagmire for analysts.
NOAA Fisheries has set an interim recovery goal of 2,500 spawners for the Snake River run. It's likely that the run has reached that number in the past couple of years, but fish managers remain tight-lipped about their latest analyses.
The upriver bright run of fall chinook headed for the Columbia's Hanford Reach has also reached epic proportions. At 160,000 chinook right now and climbing by another 2,000 to 3,000 fish every day, it will likely surpass the 1987 record of 155,000 fish.
On Sept. 18, Washington state harvest managers bumped up the daily catch limit to six chinook (up to four adult fish, all more than 12 inches) in that part of the river, saying that the McNary count "should easily exceed 200,000 adult chinook."
More than 38,000 fall chinook have already nosed past Priest Rapids Dam, heading upriver past the famous spawning grounds at Vernita Bar. Grant PUD spokesman Gary Garnant said he can't remember ever seeing that many fall chinook pass the dam--or as many sports fishermen out there, either.
About 25,000 fall chinook had passed Priest Rapids by this time last year; many spawn in the tailrace of Wanapum Dam, the next project upriver.
Jack chinook returns at McNary Dam are 23,262, a few thousand shy of last year's number by this time. This year's count may indicate that the 2001 fall migration was not the debacle that some had predicted for runs on both the Snake and the Columbia, though it's likely that survival was less for the 2001 fish. About 25 percent more smolts migrated in 2001, during the power crisis and drought when almost no water was spilled at dams to aid the summer migration.
But NOAA Fisheries' Jerry Harmon, who supervises the adult fish trap at Lower Granite said the fall run seemed pretty normal this year. He said if there are less 2-oceans this year, it hasn't been noticed by his crew. Harmon said the B-run steelhead was beginning to show in good numbers as well. Most of those fish went to sea in 2001.
Most fall chinook and steelhead were barged from the lower Snake dams to below Bonneville in 2001, but only about one-third or so of the fall chinook that reached McNary, including the outmigrants from the Hanford Reach, were barged from that site. -B.R.
 RECENT OCEAN SURVEYS SUPPORT REGIME SHIFT IN EASTERN PACIFIC
A scientific paper published last month says that the ecosystem structure of the ocean off the Columbia River has undergone a massive shift since 1998 when a strong El Nino event was followed by a rapid La Nina episode.
"The transition...was possibly the most dramatic and rapid episode of climate change in modern times," said NOAA Fisheries' researchers William Petersen and Franklin Schwing, in their paper, published in the Sept. 2003 issue of Geophysical Research Letters.
Average ocean temperatures off the Oregon coast decreased by one degree C. in 1999, while salinity increased. Coastal sea levels dropped as well, indicating stronger upwelling and a faster California Current.
The authors said plankton biomass has doubled off California since 1998, rising to values not seen since the 1970s and cold water fish like anchovies have increased by an order of magnitude, "a primary food source for adult chinook and coho salmon."
In the past several years, West Coast salmon populations have rebounded from extremely low levels, setting records in some cases.
Reduced productivity of salmon and cod in the Gulf of Alaska also tracks with the notion that a regime shift has occurred, the authors said, which has "changed ecosystem production and structure throughout the northeast Pacific Ocean." -B.R.
 HATCHERY FISH MAY NOT BE GOOD STAND-INS FOR WILD FISH
After spending millions of dollars on a four-year survival study that has tagged hundreds of thousands of hatchery spring chinook, the Fish Passage Center says that it can't tell whether the study results apply to wild fish. That's the same conclusion the center reached two years ago when it released its last report examining survival rates for transported and in-river migrating fish and tried to determine the best passage route at dams.
The latest draft report of the FPC's ongoing Comparative Survival Study indicates that overall smolt-to-adult returns [SARs] for Idaho hatchery stocks are higher than for wild fish. NOAA scientists have already noted this in their own research.
The study summary says results are "inconclusive" as to whether hatchery fish can be used as surrogates for wild fish studies. But further into the study, researchers say "early indication" from the evaluation of SARs, "suggest" the hatchery fish may not be adequate surrogates.
For the 1999 migration year, the last year to have complete data on returns, McCall Hatchery spring chinook showed a SAR above 3.5 percent for barged fish, while only 2.4 percent for fish migrating in-river (and passing dams via turbine or spillway only). The draft report estimated that wild fish had a barged SAR of 2.5 percent and an in-river SAR of 2.1 percent.
Rapid River Hatchery, the main repository for the gene pool of spring chinook blocked by Hells Canyon dams, showed SARs for the 1999 migration of 2.7 percent for barged fish and 2.4 percent for in-river fish.
But other hatcheries in the study showed lower smolt-to adult return rates. The Clearwater River's Dworshak hatchery fish had SARs of about 1 percent for both barged and in-river fish. Lookingglass Hatchery fish had barged and in-river SARS around 0.6 percent, according to the draft report.
Returns from the 2000 migration aren't yet complete, but track closely with 1999 results, showing three to four times better return rates than from the 1997 outmigration. Improved ocean conditions are generally cited as the basis for the large jump in productivity.
However, the study still ducked the issue of comparing fish survival from upriver and downriver hatcheries. That was one of its original goals and a hotly debated item during the PATH process of the late 1990s, when regional scientists wrestled with conflicting hypotheses of fish mortality and effects of dams, habitat, harvest, hatcheries and ocean conditions.
Buried deep in the CSS study is an analysis of fish returns to the Carson Hatchery on the lower Columbia River, which includes a lengthy section that tried to estimate harvest impacts, mainly by tribal fishermen, on the Carson fish.
The study estimated that 3.2 percent of the 1999 outmigration from Carson returned to Bonneville Dam, less than the 3.5 percent SAR for the barged McCall hatchery fish, which must swim about 250 miles farther upstream and pass seven more dams before they are even counted.
Some NOAA researchers had earlier concluded that such comparisons were essentially bogus because of the huge genetic differences between upriver and downriver stocks. Such differences allowed the Idaho stocks to survive in relatively austere high mountain streams, while lower river stocks were conditioned to live in warmer, low-altitude regions, the researchers said.
But that hasn't stopped the CSS folks, even though they have already dumped the results from two other lower river hatcheries from their study because of poor returns.
Their latest draft includes a special notice that says they will add PIT-tagged wild fish from the John Day River to future analyses, noting that returns from 2000 are already in the 6 percent range, "much higher than was estimated for the 2-ocean returning adults to the Snake River basin PIT-tagged chinook that also migrated in 2000."
The CSS draft has also reiterated its earlier finding that the delayed mortality of transported hatchery and wild fish, on average, is higher than for fish that migrated in-river and also higher than federal estimates used in the 2000 hydro BiOp.
By averaging survival rates across years, the CSS analysis does not get into the level of detail of recent NOAA Fisheries' survival studies, which generally show early hatchery releases have higher delayed mortality, with releases later in the migration season exhibiting survival rates similar to in-river migrating wild fish. Unfortunately, steelhead stocks, which are also listed under the ESA, do not necessarily show the same trends as spring chinook, mainly because of differences in run timing.
In fact, differences in run timing may be behind most of the survival differences noted between hatchery and wild stocks. Wild spring chinook have a much more prolonged out-migration than hatchery stocks, federal scientists say, which means they may be more susceptible to short-term adverse conditions in both the river and the near-ocean environment, such as predation by birds or other fish.
However, the CSS sponsors have asked for more money to expand their study by tagging thousands of steelhead. Their proposed budget of $1.8 million for 2004 is almost twice last year's expenditure . The Northwest Power and Conservation Council has already recommended funding the full amount. BPA's Bob Austin said discussion will take place at both policy and technical levels with the Fish Passage Center to ensure that no duplication of the tagging effort will occur with studies already underway.
Meanwhile, NOAA Fisheries' latest analyses should be out by December--updates to the "white papers" that chronicled prior federal research, including investigations into fish transportation and dam passage, that went into the 2000 hydro BiOp. Bits and pieces of the new work have shown up in technical presentations this year. They seem to indicate that transported fish, especially steelhead, are returning at higher rates than fish remaining in the river.
The updated white papers will help guide the new BiOp, which is being written after it was remanded by a federal judge last May. The judge ruled that some elements of the document, principally potential recovery actions outside the hydro system, were not reasonably certain to occur. -B.R.
 STUDY SAYS METHOW IRRIGATION CANALS RECHARGE RIVER FLOWS
A long-awaited federal study released last week seems to back up claims by Methow Basin water users that their old, leaky ditches actually improve river flows downstream. The claims have long been a rallying point for Methow residents since some have been forced by NOAA Fisheries and the Washington State Department of Ecology to improve their systems, some nearly 100 years old, to free up more water for ESA-listed salmon and steelhead.
The report by the US Geological Survey said about 73 miles of canals are found in the basin and seepage from them recharges the aquifer during late spring and summer, contributing about 38,000 acre-ft. annually to recharge in the basin. That represents about 9 percent of the annual non-fluvial (not from the river) recharge according to the agency's model.
The study says that canal seepage boosts late summer flows in the Methow River between Winthrop and Twisp about 30 cubic ft/sec., and about 10 cubic feet/sec. in the Twisp compared to winter flows. The study also found that groundwater discharge to the Methow River contributed up to 57 percent of the streamflow near its confluence with the Columbia in late summer.
When spring flows are high, the Methow and Twisp rivers recharge the aquifer considerably. In 2002, it was estimated that 137,000 acre-ft flowed into the aquifer from the Methow and about 6,400 acre-feet from the Twisp. According the USGS model, that was equal to nearly 30 percent of annual recharge by all non-fluvial sources of all the basin aquifers in 2001 and 2002.
Throughout the 1990s, federal and state authorities discounted claims by local residents that the ditches recharged the aquifer, which increased resentment against the ESA enforcers, who also gave short shrift to a 1992 USFWS study (Mullan et al) that speculated the ditches had a significant effect on river flows.
Since then, some water users have improved their delivery systems to satisfy federal requirements, but the reduced recharge has caused several lakes in the basin to begin to dry up.
"The new study backs up what we've been saying all along," said Vaughn Jolley, a director of the Methow Valley Irrigation District.
Omak Attorney Richard Price who represented the irrigation district in a recent hearing before state's Pollution Control Hearing Board said the new study would have been helpful to cite when he defended the district against the state's charge of "wasteful water practices," which the board recently upheld. Price said the USGS study might be used to supplement the record in the irrigation district's appeal, which has already been filed in superior court. -B.R.
 CRAPO CALLS FOR MEDIATION IN IDAHO WATER DISPUTE
Talks began last weekend between Idaho water users and environmental groups after Sen. Mike Crapo (R-ID) waded into the middle of their dispute and got both sides to agree to meet up in Boise.
"Nothing dramatic happened," said Norm Semanko of the Idaho Water Colaition, but he said all the issues were put on the table. "Crapo is personally committed to resolving this," he added. "He doesn't want to see litigation."
Further discussions are tentatively scheduled for next week, but it may prove to be only a temporary respite from the never-ending water wars, however. American Rivers, the National Wildlife Federation, Idaho Rivers United and the Idaho Conservation League have already threatened to sue federal agencies, saying that more of the upper Snake River water that is now used for agriculture is needed to help ESA-listed salmon migrate in the Columbia Basin.
Crapo press secretary Lindsay Nothern said his boss got involved after the Idaho Water Coalition told its members to pull out of talks with two of those same environmental groups on other water issues affecting the southern part of the state. IWC Director Semanko said earlier this month that water users wouldn't talk with environmentalists until the threat of the lawsuit was removed.
The environmental groups have since agreed to hold off on their suit for 30 days to give the Crapo talks a chance. They originally sent their "intend to sue" letter to federal agencies, including the Bureau of Reclamation, on Aug. 22, calling for re-consultation over ESA issues behind a biological opinion that governs the operations of 10 projects operated by the US Bureau of Reclamation on the upper Snake, all of which store water for agricultural use.
The Aug. 22 letter said the feds failed to conduct an adequate jeopardy analysis in the upper Snake BiOp and relied on similar "uncertain, future actions" that were cited in a recent court decision that threw out the biological opinion that covered hydro operations in the mainstem Snake and Columbia.
The letter also said that BuRec operations had failed to provide enough water to satisfy flow objectives in the hydro BiOp.
Semanko said the lawsuit had the potential to dry up 2 million acres of Idaho farmland, but the added water would still not meet lower Snake flow targets. The water coalition supports the water-for-fish policy on a "willing seller" basis.
A few days after the groups announced their intention to litigate, Semanko fired back. "They make it clear that unless Idaho officially supports breaching of downstream dams," he said, "they will sue to force the federal government to empty Idaho reservoirs of what water there is and send it all downstream as flow augmentation."
Semanko's remarks were backed by natural resource consultant Darryll Olsen. He said that if all of Idaho's water withdrawals from the Snake were used for added flow, the targets could not be reached in even average water years.
"If they're going to meet summer flow targets, they're going to have to sue God," Olsen said.
The environmental groups said they hoped to resolve their claims without litigation and asked the federal agencies to discuss the "violations" and explore settlement alternatives. Crapo spokesman Nothern said NOAA Fisheries and Bureau of Reclamation personnel were expected to take part as well.
"I have no idea what he has in mind," Justice Department Attorney Fred Disheroon said of Crapo's action. Disheroon, who is involved in the hydro BiOp lawsuit, said Crapo's involvement prompted environmental lawyers to cancel a Sept. 22 meeting to discuss peripheral issues to the hydro BiOp case among a lawyers' steering group--one of those issues being the potential lawsuit over the upper Snake BiOp.
Oregon District Court Judge James Redden, who threw out the hydro BiOp last May, has asked retired federal judge Malcolm Marsh to handle peripheral matters for him. Marsh presided over earlier BiOp lawsuits; his last major ruling supported the 1995 federal hydro BiOp that was challenged by environmental groups, some tribes and the state of Oregon. -B.R.
 GRANT PUD MEETS FISH SURVIVAL GOALS
Grant PUD officials announced Sept. 23 that recent survival studies have shown that the utility has met dam passage and reservoir goals established by fish resource agencies.
"Three years of valid studies are required in order to meet the performance standards, but we are very encouraged," said Linda Jones, Grant's manager of natural resources, regulatory affairs, and communications.
Grant spills water at its two projects during the spring and summer when ESA-listed juvenile salmon are heading to sea. Recent studies have found found that most juvenile migrants pass Wanapum Dam via its powerhouse rather than its spillway, but 70 percent to 90 percent prefer the spillway at Grant's downstream project at Priest Rapids, where about 60 percent of the river is directed every spring. Preliminary results show that about 95 percent of the juveniles passed Priest Rapids spillway safely.
With fish survival rates higher through Wanapum's turbines than its spillway, Grant says it will begin installation of advanced design turbines there next year. -B.R.
LINKS/DOCUMENTS FROM NW FISHLETTER 168:: Below are listed links and documents referred to in the text of NW Fishletter issue 168.
- Federal Defendant's First Quarterly Status Report
- Comparative Survival Study, Aug. 22, 2003
- Hydrogeology of the Unconsolidated Sediments, Water Quality, and Ground-Water/Surface-Water Exchanges in the Methow River Basin, Okanogan County, Washington, US Geological Survey, Sept. 30, 2003
THE ARCHIVE :: Previous NW Fishletter issues and supporting documents.
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