Biological Opinions - Bureau of Reclamation

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Abbreviation/Acronym KLS km LRS m Magnuson-Stevens Act MDN mi mg mg/L mm mtDNA NCRWQCB NMFS NRC NRCS NWR O&M ODEQ ODFW PCE PFMC PIT POR Project proposed action Reclamation RM RPA RPM Services SNS SONCC T&C TMDL UKL USBR USDOI USEPA USFWS USGS VSP Definition Klamath largescale suckers kilometers Lost River sucker meters Magnuson-Stevens Fishery Conservation and Management Act marine-derived nutrients miles milligrams milligrams per liter millimeters mitochondrial DNA North Coast Regional Water Quality Control Board National Marine Fisheries Service National Research Council Natural Resources Conservation Service National Wildlife Refuge operation and maintenance Oregon Department of Environmental Quality Oregon Department of Fish and Wildlife primary constituent elements Pacific Fishery Management Council passive integrated transponder period of record Klamath Project proposed operation of the Klamath Project from May 31 2013 through March 31, 2023 Bureau of Reclamation river miles reasonable and prudent alternative reasonable and prudent measure U.S. Fish and Wildlife Service and National Marine Fisheries Service shortnose sucker Southern Oregon/Northern California Coast Terms and Conditions total maximum daily load Upper Klamath Lake U.S. Bureau of Reclamation U.S. Department of Interior U.S. Environmental Protection Agency U.S. Fish and Wildlife Service U.S. Geological Survey viable salmonid population xv
Abbreviation/Acronym YTEP WDFW WRIMS WUA Yr Definition Yurok Tribal Environmental Program Washington Department of Fish and Wildlife Water Resource Integrated Modeling System weighted usable area year xvi
Page 1 and 2: National Marine Fisheries Service U
Page 3 and 4: 7.4.5 LRS and SNS Population Dynami
Page 5 and 6: 11.1.5 Critical Assumptions .......
Page 7 and 8: 16 APPENDICIES ....................
Page 9 and 10: Table 8.2 UKL end-of-month elevatio
Page 11 and 12: LIST OF FIGURES Figure 3.1. The act
Page 13 and 14: Figure 11.17. Coho salmon fry habit
Page 15: ABBREVIATIONS AND ACRONYMS Abbrevia
Page 19 and 20: In 2001, the Services issued BiOps
Page 21 and 22: Findings of Fact and Order of Deter
Page 23 and 24: proposed changes to the vegetation
Page 25 and 26: Figure 3.1. The action area for Rec
Page 27 and 28: 4 PROPOSED ACTION Reclamation propo
Page 29 and 30: 4.2 Element Two Operate the Project
Page 31 and 32: October 1 and March 1. The proposed
Page 33 and 34: Reclamation incorporated the 1981 t
Page 35 and 36: Provide Project irrigation deliveri
Page 37 and 38: Table 4.3. UKL fill rate adjustment
Page 39 and 40: Table 4.5. Calculation of fall/wint
Page 41 and 42: Flows below IGD are ultimately the
Page 43 and 44: The EWA, Project Supply, and UKL Re
Page 45 and 46: Table 4.8. Environmental Water Acco
Page 47 and 48: eleases somewhat on the ascending l
Page 49 and 50: fish disease, die off, entrainment,
Page 51 and 52: acre-feet when the Project Supply c
Page 53 and 54: Table 4.11. Monthly maximum Lower K
Page 55 and 56: 4.2.4 Ramp-Down Rates at Iron Gate
Page 57 and 58: progresses and EWA volumes are upda
Page 59 and 60: O&M activities are carried out eith
Page 61 and 62: 1. The A Canal has six headgates th
Page 63 and 64: Therefore, Reclamation proposes to
Page 65 and 66: coordinate with the NMFS to develop
Page 67 and 68:
the confluence with Omogar Creek at
Page 69 and 70:
though several major improvements t
Page 71 and 72:
Sucker larvae transform into age-0
Page 73 and 74:
units: (1) Clear Lake; (2) Tule Lak
Page 75 and 76:
Figure 7.2. Adult spawning populati
Page 77 and 78:
Table 7.1. Estimated LRS and SNS ad
Page 79 and 80:
1905, Ch. 567, 33 Stat. 714). The P
Page 81 and 82:
Figure 7.4 Modeled April through No
Page 83 and 84:
7.9.2 Klamath Basin The Oregon Clim
Page 85 and 86:
A change in mean precipitation rang
Page 87 and 88:
Table 7.2 Impaired water bodies wit
Page 89 and 90:
Table 7.3 Seasonal comparisons of p
Page 91 and 92:
ammonia that is lethal to 50 percen
Page 93 and 94:
Table 7.4 Estimated external phosph
Page 95 and 96:
examination of juvenile suckers fro
Page 97 and 98:
Evaluation of baseline hydrology in
Page 99 and 100:
2012 1931 through 2012 12.6% 0.24 5
Page 101 and 102:
The overall water year trend (Table
Page 103 and 104:
Figure 7.7 Sprague River trends, wa
Page 105 and 106:
Figure 7.9 Sprague River trends, wa
Page 107 and 108:
Figure 7.12 Williamson River trends
Page 109 and 110:
Figure 7.14 UKL trends, water years
Page 111 and 112:
Figure 7.17 UKL: net inflow departu
Page 113 and 114:
7.10.3.3 Competition and Predation
Page 115 and 116:
By late July, surviving larval suck
Page 117 and 118:
Threat Nature of Threat Life Stage
Page 119 and 120:
2011) and increased adult spawning
Page 121 and 122:
Based on the best available informa
Page 123 and 124:
contrast, water levels began 1.5 ft
Page 125 and 126:
evaporation and seepage estimated a
Page 127 and 128:
prolonged low oxygen conditions if
Page 129 and 130:
The April through September 4,034.6
Page 131 and 132:
8 EFFECTS OF THE ACTION ON LOST RIV
Page 133 and 134:
Although the volume of Project wate
Page 135 and 136:
than 1 m), and fitting one or more
Page 137 and 138:
Figure 8.3. UKL elevations at the e
Page 139 and 140:
Services and Reclamation will deter
Page 141 and 142:
For cumulative net inflow values be
Page 143 and 144:
Figure 8.8. UKL elevations at the e
Page 145 and 146:
Figure 8.10. UKL elevations at the
Page 147 and 148:
Figure 8.12. UKL elevations at the
Page 149 and 150:
natural and man-caused changes in i
Page 151 and 152:
Table 8.1 UKL end-of-month surface
Page 153 and 154:
UKL. Based on best available inform
Page 155 and 156:
larvae in UKL. Annual production of
Page 157 and 158:
Table 8.5 UKL end-of-month elevatio
Page 159 and 160:
Based on our review of the literatu
Page 161 and 162:
into the Pelican Bay water quality
Page 163 and 164:
We assume that UKL surface elevatio
Page 165 and 166:
vary by several orders of magnitude
Page 167 and 168:
survival rates, we know that some o
Page 169 and 170:
populations, and contains the large
Page 171 and 172:
8.3.5.1 Effects to Adult Sucker Spa
Page 173 and 174:
Table 8.8 Clear Lake surface elevat
Page 175 and 176:
occur, especially in the west lobe.
Page 177 and 178:
Table 8.9 End of the month surface
Page 179 and 180:
8.3.7.4 Effects of Entrainment Loss
Page 181 and 182:
The source of the sediment is unkno
Page 183 and 184:
period when they migrate upstream t
Page 185 and 186:
limited LRS and SNS persistence in
Page 187 and 188:
term and localized and because fish
Page 189 and 190:
8.5.1 Canal Salvage Reclamation pro
Page 191 and 192:
high predation rates and failure of
Page 193 and 194:
include the Klamath Basin Rangeland
Page 195 and 196:
Figure 9.1 Designated CHUs for the
Page 197 and 198:
These are discussed in greater deta
Page 199 and 200:
The proposed action will have no ef
Page 201 and 202:
No other spawning habitat exists be
Page 203 and 204:
consulted on. Current monitoring da
Page 205 and 206:
proposed action and this PCE suppor
Page 207 and 208:
Because of a multi-decade lack of r
Page 209 and 210:
Adverse effects of the proposed act
Page 211 and 212:
that juvenile survival is most like
Page 213 and 214:
elocation effort in Lake Ewauna to
Page 215 and 216:
LRS and SNS population resiliency o
Page 217 and 218:
stratum 4 (Interior Klamath) in whi
Page 219 and 220:
Pacific salmonids Oncorhynchus spp.
Page 221 and 222:
scenario, actions and elements of t
Page 223 and 224:
flow prescriptions should mimic pro
Page 225 and 226:
11.2.1 Current Condition of Critica
Page 227 and 228:
11.2.2 Factors Affecting SONCC Coho
Page 229 and 230:
e disoriented or displaced downstre
Page 231 and 232:
enhancement, and rehabilitative act
Page 233 and 234:
Water Temperature Sedimentation Org
Page 235 and 236:
Figure 11.1 Longitudinal and season
Page 237 and 238:
functioning floodplains that fail t
Page 239 and 240:
downstream of IGD, (2) enhance coho
Page 241 and 242:
few local ranchers and water distri
Page 243 and 244:
in some tributaries, access to and
Page 245 and 246:
11.3.7 Summary of Critical Habitat
Page 247 and 248:
these two time periods, the effects
Page 249 and 250:
consists of approximately 29,000 ac
Page 251 and 252:
The PacifiCorp habitat conservation
Page 253 and 254:
IGD, or used in constructed habitat
Page 255 and 256:
estoration, watershed planning, sal
Page 257 and 258:
Table 11.4. Modeled suspended sedim
Page 259 and 260:
parasites Ceratomyxa shasta (causes
Page 261 and 262:
that become infected is estimated t
Page 263 and 264:
where snow water equivalent is proj
Page 265 and 266:
minimizing disease risks, the detai
Page 267 and 268:
Figure 11.4. Proposed action, histo
Page 269 and 270:
Figure 11.6. Proposed action weekly
Page 271 and 272:
Figure 11.9. Regression between EWA
Page 273 and 274:
Figure 11.11. Proposed action and o
Page 275 and 276:
Figure 11.12. Number of days per wa
Page 277 and 278:
Figure 11.14. Monthly coefficient o
Page 279 and 280:
IGD. The proposed action modeled da
Page 281 and 282:
The results from Table 11.7 indicat
Page 283 and 284:
likely to increase the quantity of
Page 285 and 286:
habitat decreases between the Shast
Page 287 and 288:
Table 11.9. Daily average mainstem
Page 289 and 290:
Table 11.10. Daily average mainstem
Page 291 and 292:
5% 3336 13176 27664 26168 30946 237
Page 293 and 294:
The proposed action results in agri
Page 295 and 296:
Figure 11.21. Monthly mean of daily
Page 297 and 298:
Riparian restoration projects will
Page 299 and 300:
expected to be typical riparian spe
Page 301 and 302:
Table 11.13. Annual percent of proj
Page 303 and 304:
esource needs as they grow, and 3)
Page 305 and 306:
11.5.2 Klamath River Basin Adjudica
Page 307 and 308:
coho salmon within the Klamath Rive
Page 309 and 310:
aspects of a natural flow regime th
Page 311 and 312:
element of coho salmon critical hab
Page 313 and 314:
12.1.1.1 Risk Analyses for Endanger
Page 315 and 316:
ESU DIVERSITY STRATA POPULATIONS IN
Page 317 and 318:
eproduction, and distribution. The
Page 319 and 320:
Figure 12.2. Historic population st
Page 321 and 322:
the average ratio of IP-km to total
Page 323 and 324:
Although long-term data on coho sal
Page 325 and 326:
1980 1981 1982 1983 1984 1985 1986
Page 327 and 328:
maintain viable abundances in many
Page 329 and 330:
12.2.5.5 Viability Summary Though p
Page 331 and 332:
coastal currents and upwelling, kno
Page 333 and 334:
12.2.6.2 Marine Derived Nutrients M
Page 335 and 336:
fisheries south of Cape Falcon, Ore
Page 337 and 338:
12.3 Environmental Baseline of Coho
Page 339 and 340:
water temperatures up to 19 ºC in
Page 341 and 342:
some coho salmon smolts may stop mi
Page 343 and 344:
threshold, all Klamath River coho s
Page 345 and 346:
abundance threshold (Table 12.3). T
Page 347 and 348:
mainstem Klamath and Trinity rivers
Page 349 and 350:
Although there are risks to Klamath
Page 351 and 352:
activities are generally beneficial
Page 353 and 354:
12.4 Effects to Individuals The pro
Page 355 and 356:
12.4.1.2 Response 12.4.1.2.1 Adults
Page 357 and 358:
(2012) believes is representative o
Page 359 and 360:
genotype II density of 5 spores/L w
Page 361 and 362:
flows provide a limit to the increa
Page 363 and 364:
polychaete and sediment disturbance
Page 365 and 366:
which will likely result in a relat
Page 367 and 368:
etween Trees of Heaven (RM 172) and
Page 369 and 370:
action. Reclamation estimated that
Page 371 and 372:
Based on literature, increased comp
Page 373 and 374:
Table 12.6. Summary of risks result
Page 375 and 376:
most juveniles. Stream flow diversi
Page 377 and 378:
at most fish relocation sites, base
Page 379 and 380:
higher, the minimally increased sed
Page 381 and 382:
Small pulses of moderately turbid w
Page 383 and 384:
Boulder faces in the deflector stru
Page 385 and 386:
conditions may fail if those condit
Page 387 and 388:
Adverse effects of the proposed act
Page 389 and 390:
Potential Stressor Habitat Reductio
Page 391 and 392:
Potential Stressor Elevated water t
Page 393 and 394:
12.6.2 Effects of fitness consequen
Page 395 and 396:
13 INCIDENTAL TAKE STATEMENT Sectio
Page 397 and 398:
Table 13.1 Summary of maximum annua
Page 399 and 400:
in fewer larvae and juveniles, and
Page 401 and 402:
Table 13.2 Estimated annual maximum
Page 403 and 404:
1.2.1.8. Incidental Take Caused by
Page 405 and 406:
characteristics of aquatic species,
Page 407 and 408:
Table 13.5 Expected annual Environm
Page 409 and 410:
Cause of Incidental Take Habitat Re
Page 411 and 412:
Clear Lake, Gerber Reservoir, and T
Page 413 and 414:
This term and condition is requirin
Page 415 and 416:
13.4 Mandatory Monitoring and Repor
Page 417 and 418:
Required hydrologic monitoring incl
Page 419 and 420:
Table 13.7. Summary of LRS and SNS
Page 421 and 422:
T&C or Mandatory Monitoring Mandato
Page 423 and 424:
Table 13.9 Summary of reporting and
Page 425 and 426:
Table 13.10 Summary of meetings req
Page 427 and 428:
the above QA/QC procedures describe
Page 429 and 430:
Barry, P.M., E.C. Janney, D.A. Hewi
Page 431 and 432:
Burdick, S.M. and J. Rasmussen. 201
Page 433 and 434:
Dunsmoor, L., L. Basdekas, B. Wood,
Page 435 and 436:
Garen, D. 2011, Upper Klamath Basin
Page 437 and 438:
Janney, E.C., B.S. Hayes, D.A. Hewi
Page 439 and 440:
Laenen, A., and A.P. LeTourneau. 19
Page 441 and 442:
Miller, R.R., and G.R. Smith. 1981.
Page 443 and 444:
Perkins, D.L., and G.G. Scoppettone
Page 445 and 446:
(Deltistes luxatus) in Tule and Cle
Page 447 and 448:
Terwilliger, M. 2006. Physical habi
Page 449 and 450:
USBR [U.S. Bureau of Reclamation].
Page 451 and 452:
Williams, J.E. 2000. Chapter 13. Th
Page 453 and 454:
Arthington, A.H., S.E. Bunn, N.L. P
Page 455 and 456:
Beeman, J., S. Juhnke, G. Stutzer a
Page 457 and 458:
Brommer, J.E. 2000. The evolution o
Page 459 and 460:
Department of the Army Regional Gen
Page 461 and 462:
Chilcote, M. W. 2003. Relationship
Page 463 and 464:
Dunsmoor LK, and Huntington CW. 200
Page 465 and 466:
Foott, J.S., R. Stone, E. Wiseman,
Page 467 and 468:
Habera, J.W., R.J. Strange, B.D. Ca
Page 469 and 470:
Hemstreet, T. 2013. Electronic mail
Page 471 and 472:
Jordan, M. S. 2012. Hydraulic predi
Page 473 and 474:
Kostow, K. E., A. R. Marshall and S
Page 475 and 476:
MacFarlane, R. B., S. Hayes, and B.
Page 477 and 478:
Moyle, P. B. 2002. Inland Fishes of
Page 479 and 480:
PacifiCorp Klamath Hydroelectric Pr
Page 481 and 482:
Oregon Department of Environmental
Page 483 and 484:
Puckridge, J. T., F. Sheldon, K. F.
Page 485 and 486:
Ring, T.E. and B. Watson. 1999. Eff
Page 487 and 488:
Sommer, T. R., M. L. Nobriga, W. C.
Page 489 and 490:
Taylor, R. 1991. A review of local
Page 491 and 492:
USFWS [U. S. Fish and Wildlife Serv
Page 493 and 494:
Ward G, and Armstrong N. 2010. Asse
Page 495 and 496:
Winker, K., J. H. Rappole, and M. A
Page 497 and 498:
77 FR 476. National Marine Fisherie
Page 499 and 500:
UKL Elevation (feet) Active Storage
Page 501 and 502:
Page 503 and 504:
Page 505 and 506:
16.2 Appendix B: Elevation Flow Dat
Page 507 and 508:
490
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Week of Water Year 1981 1982 1983 1
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Water Year October November Decembe
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16.3 Appendix C: Description of Res
Page 535 and 536:
4. Removal of Small Dams (permanent
Page 537 and 538:
Information regarding consideration
Page 539 and 540:
9. Piping Ditches a. Project Descri
Page 541 and 542:
. Site-Specific Restrictions Restri
Page 543 and 544:
6. Protection Measures The followin
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to enter or be placed where they co
Page 547 and 548:
shall be distributed throughout the
Page 549 and 550:
weed free straw, silt fences) are i
Page 551 and 552:
the project is located, and compris
Page 553 and 554:
2. Post Construction Monitoring and
Page 555 and 556:
Median Seasonal Flow (acre-feet) Me
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Median Seasonal Net Inflow (acre-fe
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16.5 Appendix E: Observed and Model
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Observed and modeled proposed actio
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Observed and modeled proposed actio
Page 603 and 604:
16.6 Appendix F: Analyzing the rela
Page 605 and 606:
Table 1. Paired comparison of the c
Page 607:
Table 3. The difference in the mean
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