Regulatory Division Floor San Francisco, CA 94103-1398 .
Regulatory Division1455 Market Street, 16th FloorSan Francisco, CA 94103-1398SAN FRANCISCO DISTRICTPUBLIC NOTICEPROJECT: Bel Marin Keys Maintenance DredgingPUBLIC NOTICE NUMBER: 2006-22397NPUBLIC NOTICE DATE: June 9, 2017COMMENTS DUE DATE: June 30, 2017PERMIT MANAGER: Mark D’AvignonTELEPHONE: 415-503-68061. INTRODUCTION:The Bel Marin KeysCommunity Services District (BMKCSD), 4 MontegoKey, Novato, California (contact: Noemi CamargoMartinez; phone: (415) 883-4222), through its agent,CLE Engineering, 10 Commercial Boulevard, Suite100, Novato, California 94949 (contact: WendyRocha, phone: (508) 642-2469) has applied to the U.S.Army Corps of Engineers (Corps), San FranciscoDistrict, for a 10-year Department of the Army Permitto carry out maintenance dredging of accumulatedsediment, with upland disposal at the Bel Marin KeysDredged Material Management Site (BMK DMMS),in the Bel Marin Keys North Lagoon and NovatoCreek in Novato, Marin County, California. Thepurpose of the proposed maintenance dredging is toreturn the Bel Marin Keys Lagoon and designated areaswithin Novato Creek, to the originally permitted designdepth to allow safe navigational depths for recreationalboats and water level management within the Bel MarinKeys Lagoons. This Department of the Army Permitapplication is being processed pursuant to theprovisions of Section 404 of the Clean Water Act of1972, as amended (33 U.S.C. § 1344 et seq.) andSection 10 of the Rivers and Harbors Act of 1899, asamended (33 U.S.C. § 403 et seq).E-MAIL: mark.r.d’avignon@usace.army.milProject Site Description: The proposed projectsite is located at the Bel Marin Keys Development(BMK), which consists of approximately 702 singlefamily homes. The BMK is surrounded by open spaceand bounded by tidal wetlands to the south, NovatoCreek to the east and west, and managed farm land tothe north and northeast. The BMK surrounds twoman-made lagoons, each in approximately 100 acresin area, that open to Novato Creek via boat locks andculverts. The BMK Lagoons and Novato Creek arehabitat for native fish including federally-listedspecies such as steelhead and green sturgeon, and areconsidered essential fish habitat (EFH) by the NationalMarine Fisheries Service (See Section on theMagnuson-Stevens Fishery Conservation andManagement Act below.). The substrate within theBMK Lagoons and Novato Creek consists primarily ofrecently deposited silt and clay. Submerged aquaticvegetation, specifically eelgrass, is not believed to bepresent within the BMK Lagoons or Novato Creek.Project Description: As shown in the attacheddrawings, the applicant plans to remove approximately24,774 cubic yards (cys) of sediment from the 7-acre(approximately) dredge footprint within the NorthLagoon and Novato Creek in an initial episode and atotal of approximately 100,000 cys from the BMKLagoons and Novato Creek over the life of the permit.Existing depths range from 0 to 5 feet mean lower low(MLLW). The design depths for the BMK Lagoon andNovato Creek dredge areas is -2.5 feet MLLW plus anadditional 1-foot overdredge allowance. The dredgedmaterial would be removed using a hydraulic dredgeand pumped, via a dredged material slurry pipeline, to2. PROPOSED PROJECT:Project Site Location: As shown in the attachedproposed-project plans and drawings, the Bel MarinKeys Lagoons and the BMK DMMS are located eastof Highway 101 south of Highway 37 adjacent toNovato Creek on the western shoreline of San PabloBay in Novato, Marin County, California.1
the 22-acre BMK DMMS site. The BMK DMMS is apermitted dredged material placement site located justwest of the BMK on BMK Boulevard and adjacent toNovato Creek. Dredged material placed within theBMK DMMS would be allowed to settle and clarifiedreturn-water would be released into Novato Creek via aculvert at the northeast corner of the site. The BMKDMMS was originally constructed in 1985, and wasenhanced and used again in 2005 for the last majordredging episode at the BMK, which involvedplacement of approximately 80,000 cys of sediment.Dredged material placed at the BMK DMMS will bereused for tidal wetland creation, levee maintenance, orother appropriate beneficial reuses.purpose is the disposal of dredged material frommaintenance dredge projects in the San Francisco BayRegion consistent with the adopted LTMS (LongTerm Management Strategy for the Placement ofDredged Material in the San Francisco Bay Region)EIR/EIS and LTMS Management Plan of 2001.Project Impacts The proposed maintenancedredging of the BMK North Lagoon and Novato Creekdredge areas would result in the placement (i.e.discharge) of approximately 100,000 cubic yards ofsediment (i.e. dredged material) over the life of thepermit and approximately 24,774 cubic yards in theinitial dredging episode. The proposed project wouldtemporarily disturb up to approximately 7 acres of thesubstrate and associated benthic organisms (i.e.benthos) within the BMK North Lagoon and NovatoCreek in the initial dredge episode. However, it isexpected the substrate and benthos would return topre-dredging conditions relatively soon after dredgingstops. Fish species utilizing the boat basins for feedingand protection from predators would be temporarilydisplaced by dredging activities, but would be able tofind similar foraging opportunities and protectionfrom predators in the adjacent aquatic habitat inNovato Creek and San Pablo Bay.Prior to each dredging episode, the Dredge MaterialManagement Office (DMMO) will evaluate thesediments to be dredged for disposal or reuse suitability.The DMMO includes representatives from the U.S.Environmental Protection Agency, San Francisco BayConservation and Development Commission(BCDC), San Francisco Bay Regional Water QualityControl Board (RWQCB), and the U.S. Army Corpsof Engineers. The DMMO is tasked with approvingsampling and analysis plans in conformity with testingmanuals, reviewing the test results and reachingconsensus regarding a suitable disposition for thematerial.According to existing eelgrass survey maps, theBMK Lagoons and Novato Creek are not known tocontain stands of eelgrass, which is a submergedaquatic plant of ecological importance in SanFrancisco Bay and identified by the National MarineFisheries Service (NMFS) as essential fish habitat(EFH) (See Section on the Magnuson-Stevens FisheryConservation and Management Act below.).Therefore, removal of eelgrass beds due to dredging isnot expected to occur. There are no known eelgrassbeds in close proximity (i.e. within 250 meters) to theproposed dredging site, therefore, indirect effects toeelgrass due to turbidity and siltation are not expectedto occur from the proposed dredging activity.Basic Project Purpose: The basic project purposecomprises the fundamental, essential, or irreduciblepurpose of the project, and is used by the Corps todetermine whether the project is water dependent.Although the purpose of the project, as stated above,is for safe navigational depths, for consideration inSection 404(b)(1) (Clean Water Act), the basicpurpose of the project is the disposal of dredgedmaterial.Overall Project Purpose: The overall projectpurpose serves as the basis for the Section 404(b)(1)alternatives analysis, and is determined by furtherdefining the basic project purpose in a manner thatmore specifically describes the applicant's goals forthe project, while allowing a reasonable range ofalternatives to be analyzed. The overall projectThe detrimental effects on erosion/sedimentationrates, substrate, water quality, fish habitat, air quality,and noise are all expected to be minor and short term.No permanent negative effects such as undesired2
substrate alteration, decreased water quality, loss offish habitat, decrease air quality, and noise pollutionare anticipated. The beneficial effects on economics,employment, removal of contaminants, safety, andnavigation are major and long term.Coastal zone management issues should bedirected to the Executive Director, San Francisco BayConservation and Development Commission, 455Golden Gate Avenue, Suite 10600, San Francisco,California 94102, by the close of the comment period.3. STATE AND LOCAL APPROVALS:4. COMPLIANCE WITH VARIOUS FEDERALLAWS:Water Quality Certification: State water qualitycertification or a waiver is a prerequisite for theissuance of a Department of the Army Permit toconduct any activity which may result in a fill orpollutant discharge into waters of the United States,pursuant to Section 401 of the Clean Water Act of1972, as amended (33 U.S.C. § 1341 et seq.). Theapplicant has recently submitted an application to theCalifornia Regional Water Quality Control Board(RWQCB) to obtain water quality certification for theproject. No Department of the Army Permit will beissued until the applicant obtains the requiredcertification or a waiver of certification. A waiver canbe explicit, or it may be presumed if the RWQCB failsor refuses to act on a complete application for waterquality certification within 60 days of receipt, unlessthe District Engineer determines a shorter or longerperiod is a reasonable time for the RWQCB to act.National Environmental Policy Act (NEPA):Upon review of the Department of the Army Permitapplication and other supporting documentation, theCorps has made a preliminary determination that theproject neither qualifies for a Categorical Exclusionnor requires the preparation of an EnvironmentalImpact Statement for the purposes of NEPA. At theconclusion of the public comment period, the Corpswill assess the environmental impacts of the project inaccordance with the requirements of the NationalEnvironmental Policy Act of 1969 (42 U.S.C. §§4321-4347), the Council on Environmental Quality'sRegulations at 40 C.F.R. Parts 1500-1508, and theCorps Regulations at 33 C.F.R. Part 325. The finalNEPA analysis will normally address the direct,indirect, and cumulative impacts that result fromregulated activities within the jurisdiction of the Corpsand other non-regulated activities the Corpsdetermines to be within its purview of federal controland responsibility to justify an expanded scope ofanalysis for NEPA purposes. The final NEPA analysiswill be incorporated in the decision documentationthat provides the rationale for issuing or denying aDepartment of the Army Permit for the project. Thefinal NEPA analysis and supporting documentationwill be on file with the San Francisco District,Regulatory Division.Water quality issues should be directed to theExecutive Officer, California Regional Water QualityControl Board, San Francisco Bay Region, 1515 ClayStreet, Suite 1400, Oakland, California 94612 by theclose of the comment period.Coastal Zone Management: Section 307(c) ofthe Coastal Zone Management Act of 1972, asamended (16 U.S.C. § 1456(c) et seq.), requires a nonfederal applicant seeking a federal license or permit toconduct any activity occurring in or affecting thecoastal zone to obtain a Consistency Certification thatindicates the activity conforms with the state’s coastalzone management program. Generally, no federallicense or permit will be granted until the appropriatestate agency has issued a Consistency Certification orhas waived its right to do so.Endangered Species Act (ESA): Section 7(a)(2)of the ESA of 1973, as amended (16 U.S.C. § 1531 etseq.), requires federal agencies to consult with eitherthe U.S. Fish and Wildlife Service (USFWS) orNMFS, or both, to insure actions authorized, funded,or undertaken by the agency are not likely tojeopardize the continued existence of any federallylisted species or result in the adverse modification ofdesignated critical habitat. Based on this review, the3
Corps has made a preliminary determination that thefollowing federally-listed species and designatedcritical habitat are present at the project location or inits vicinity, and may be affected by projectimplementation.North Bay might enter the MYC boat basin. Sinceimpacts to the water column during disposal eventswould be short-term, localized and minor in magnitude,no potentially adverse effects to steelhead that may benear the disposal site are anticipated, if the dredge workis conducted within the permitted work window.Sacramento River winter-run Chinook salmon(Oncorhynchus tshawytscha) were federally-listed asendangered on January 4, 1994 (59 Fed. Reg.442).Adult winter-run Chinook salmon migrate through SanFrancisco Bay, as well as Suisun Bay and Honker Bay,to spawning areas in the upper Sacramento River duringthe late fall and early winter. Juveniles traveldownstream through San Francisco Bay to the PacificOcean in the late fall as well. The movements of adultand juvenile salmon through the Bay system are thoughtto be rapid during these migrations. Since impacts to thewater column during disposal events would be shortterm, localized and minor in magnitude, no potentiallyadverse effects to winter-run Chinook salmon that maybe near the disposal site are anticipated, if the dredgework is conducted within the permitted work window.The Central Valley California Distinct PopulationSegment (DPS) steelhead (Oncorhynchus mykiss) wasfederally-listed as threatened on March 19, 1998 (63FR 13347), and were reconfirmed as threatened onJanuary 5, 2006 (71 FR 834). Critical habitat forcentral valley California steelhead was designated onSeptember 2, 2005 (70 FR 52488). The DPS includesall naturally spawned populations of steelhead (andtheir progeny) in the Sacramento and San JoaquinRivers and their tributaries. Excluded are steelheadfrom San Francisco and San Pablo Bays and theirtributaries. All Central Valley steelhead are currentlyconsidered winter steelhead. Juvenile steelheads livein freshwater between one and four years, then becomesmolts and migrate to the sea from November throughMay.Central Valley Spring-Run ESU Chinook salmon(Oncorhynchus tshawytscha) were listed as threatenedon September 16, 1999 (64 FR 50394). Spring-runChinook salmon typically migrate upstream throughSan Francisco Bay to spawning areas between Marchand July. Spawning usually occurs between lateAugust and early October with a peak in September.Juveniles travel downstream through San Francisco Bayin late fall to spring and then to the Pacific Ocean oncethey have undergone smoltification. Since impacts tothe water column during disposal events would be shortterm, localized and minor in magnitude, no potentiallyadverse effects to spring-run Chinook salmon that maybe near the disposal site are anticipated, if the dredgework is conducted within the permitted work window.On July 6, 2006, NMFS listed the North Americangreen sturgeon (Acipenser medirosrtis) south of the EelRiver in California as threatened under the EndangeredSpecies Act (71 Fed. Reg. 17757). The Corps hasinitiated consultation per Section 7 of the ESAregarding this species. If a permit is issued for thisproposed project it will contain any special conditionsresulting from that consultation.Habitat for Ridgway’s rail (Rallus obsoletus) hasbeen identified along portions of Novato Creek in thevicinity of Bel Marin Keys. In order to avoid potentialimpacts to Ridgway’s rail, dredging in Novato Creek,or within 250 feet of known nesting habitat forRidgway’s rail, shall occur from September 1 toNovember 30 in order to avoid the breeding season ofthe Ridgway’s railCentral California populations of steelhead trout(Oncorhynchus mykiss) were federally classified asthreatened in August 1997. The steelhead that occur inSan Francisco Bay are included in this distinctpopulation segment and therefore receive protectionunder the Endangered Species Act. There is concern thatsteelhead migrating through the Bay to streams in theAdditionally, the Corps has concerns regardingpotential impacts to Pacific herring during its annualspawning season. The proposed maintenance dredgingwill occur within the traditional Pacific herring4
spawning grounds. As a result, the Corps will conditionthe permit (if issued) so that dredging will be allowedonly from March 1 through November 30 in any year.the Coastal Pelagic and/or the Pacific Coast SalmonFMPs.The Corps and NMFS completed a programmaticEFH consultation on June 9, 2011 for maintenancedredging. One of NMFS’s key concerns with dredgingis potential impacts to eelgrass beds. The “BaywideEelgrass Inventory of San Francisco Bay,” preparedby Merkel and Associates, dated October 2010, doesnot show eelgrass beds within 250 meters of the BelMain Keys Lagoon and Novato Creek. Therefore, theapplicant would not be required to deploy silt curtainsin order to minimize adverse effects upon eelgrassfrom turbidity created from the disturbance ofsediment during dredging operations.Please note that programmatic biological opinions(BOs) were issued by USFWS (March 12, 1999) andNMFS (July 9, 2015) for the LTMS. As a result of theBOs there are allowable time frames to dredge toprotect threatened and endangered species and theirdesignated critical habitat per Section 7 of theEndangered Species Act of 1973, as amended. If apermit is issued for this proposed project it will containa condition that dredging and disposal operations shalloccur only from September 1 through November 30.Dredging outside the LTMS environmental workwindow of September 1 through November 30 wouldrequire consultation with the National MarineFisheries Service (NMFS) (pursuant to Section 7 ofthe Endangered Species Act) and approval from theNMFS and the U.S. Army Corps of Engineers. If thedredge work is conducted within those time frames,there is no need for consultation.The recently-deposited bottom sediments to bedredged during maintenance dredge activities arecomposed mainly (approximately 95%) of silts andclays (mud). It is presumed that fish species utilizingthe area would be using it for feeding during a periodof growth. When dredging occurs, the fish should beable to find ample and suitable foraging areas in theadjacent marine habitat of Novato Creek and SanPablo Bay. As the infaunal community recovers in thedredged area, fish species will return to feed.Therefore, the proposed dredging is expected to haveonly short-term, minor adverse effects on EFH.Magnuson-Stevens Fishery Conservation andManagement Act (MSFCMA): Section 305(b)(2) ofthe MSFCMA of 1966, as amended (16 U.S.C. § 1801et seq.), requires federal agencies to consult with theNational Marine Fisheries Service (NMFS) on allproposed actions authorized, funded, or undertaken bythe agency that may adversely affect essential fishhabitat (EFH). EFH is defined as those waters andsubstrate necessary to fish for spawning, breeding,feeding, or growth to maturity. EFH is designatedonly for those species managed under a FederalFisheries Management Plan (FMP), such as the PacificGroundfish FMP, the Coastal Pelagics FMP, and thePacific Coast Salmon FMP. As the federal lead agencyfor this project, the Corps has conducted a review ofdigital maps prepared by NMFS depicting EFH todetermine the presence or absence of EFH in theproject area. Based on this review, the Corps has madea preliminary determination that EFH is present at theproject location or in its vicinity, and that the criticalelements of EFH may be adversely affected by projectimplementation. The proposed project is locatedwithin an area managed under the Pacific Groundfish,National Historic Preservation Act (NHPA):Section 106 of the NHPA of 1966, as amended (16U.S.C. § 470 et seq.), requires federal agencies toconsult with the appropriate State HistoricPreservation Officer to take into account the effects oftheir undertakings on historic properties listed in oreligible for listing in the National Register of HistoricPlaces. Section 106 of the NHPA further requiresfederal agencies to consult with the appropriate TribalHistoric Preservation Officer or any Indian tribe totake into account the effects of their undertakings onhistoric properties, including traditional culturalproperties, trust resources, and sacred sites, to whichIndian tribes attach historic, religious, and culturalsignificance.5
Because the Bel Marin Keys North Lagoon andNovato Creek dredging areas have been previouslydredged, historic or archeological resources are notexpected to occur in the project vicinity. If unrecordedarchaeological resources are discovered during projectimplementation, those operations affecting suchresources will be temporarily suspended until theCorps concludes Section 106 consultation with theState Historic Preservation Officer or the TribalHistoric Preservation Officer to take into account anyproject related impacts to those resources.6. PUBLIC INTEREST EVALUTION:Thedecision on whether to issue a Department of the ArmyPermit will be based on an evaluation of the probableimpacts, including cumulative impacts, of the projectand its intended use on the public interest. Evaluationof the probable impacts requires a careful weighing ofthe public interest factors relevant in each particularcase. The benefits that may accrue from the projectmust be balanced against any reasonably foreseeabledetriments of project implementation. The decision onpermit issuance will, therefore, reflect the nationalconcern for both protection and utilization ofimportant resources. Public interest factors whichmay be relevant to the decision process vironmental concerns, wetlands, cultural values,fish and wildlife values, flood hazards, floodplainvalues, land use, navigation, shore erosion andaccretion, recreation, water supply and conservation,water quality, energy needs, safety, food and fiberproduction, mineral needs, considerations of propertyownership, and, in general, the needs and welfare ofthe people.5. COMPLIANCE WITH THE SECTION404(b)(1) GUIDELINES: Projects resulting indischarges of dredged or fill material into waters of theUnited States must comply with the Guidelinespromulgated by the Administrator of theEnvironmental Protection Agency under Section404(b) of the Clean Water Act (33 U.S.C. § 1344(b)).An evaluation pursuant to the Guidelines indicates thedisposal of dredged material is not dependent onlocation in or proximity to waters of the United Statesto achieve the basic project purpose. This conclusionraises the (rebuttable) presumption of the availabilityof a less environmentally damaging practicablealternative to the project that does not require thedischarge of dredged or fill material into waters of theU.S.7. CONSIDERATION OF COMMENTS: TheCorps is soliciting comments from the public; federal,state and local agencies and officials; Native AmericanNations or other tribal governments; and otherinterested parties in order to consider and evaluate theimpacts of the project. All comments received by theCorps will be considered in the decision on whether toissue, modify, condition, or deny a Department of theArmy Permit for the project. To make this decision,comments are used to assess impacts on endangeredspecies, historic properties, water quality, and otherenvironmental or public interest factors addressed in afinal environmental assessment or environmentalimpact statement. Comments are also used todetermine the need for a public hearing and todetermine the overall public interest of the project.On October 29, 2004 the U.S. Army Corps ofEngineers, U.S. Environmental Protection Agency,San Francisco Bay Conservation and DevelopmentCommission, and the San Francisco Bay RegionalWater Quality Control Board adopted the “SmallDredger Programmatic Alternatives Analysis(SDPAA) for Disposal of Maintenance DredgedMaterial in the San Francisco Bay Region.” Due tothe limited disposal alternatives in the San FranciscoBay region, small dredgers (as defined in the SDPAA)are not required to submit an alternatives analysis fordisposal of maintenance-dredged material. The BMKis included in the list of small dredgers in the SDPAA.8. SUBMITTING COMMENTS:During thespecified comment period, interested parties maysubmit written comments to Mark D’Avignon, SanFrancisco District, Operations and ReadinessDivision, 1455 Market Street, 16th Floor, San6
Francisco, California 94103-13978; comment lettersshould cite the project name, applicant name, andpublic notice number to facilitate review by the PermitManager. Comments may include a request for apublic hearing on the project prior to a determinationon the Department of the Army permit application;such requests shall state, with particularity, the reasonsfor holding a public hearing.All substantivecomments will be forwarded to the applicant forresolution or rebuttal. Additional project informationor details on any subsequent project modifications ofa minor nature may be obtained from the applicantand/or agent, or by contacting the Permit Manager bytelephone or e-mail cited in the public noticeletterhead. An electronic version of this public noticemay be viewed under the Current Public Notices tabon the US Army Corps of Engineers, S. F. ions/Regulatory.7
sediment, with upland disposal at the Bel Marin Keys Dredged Material Management Site (BMK DMMS), in the Bel Marin Keys North Lagoon and Novato Creek in Novato, Marin County, California. The purpose of the proposed maintenance dredging is to return the Bel Marin Keys Lagoon and designated areas
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