Comment Number

Comment Category

Nature of Science Panel Comment

Phase 2 Scope of Work

Recommendations

1

1

Conduct a comprehensive research program designed to advance basic understanding of the natural processes of the Bay and the human influences on those processes. Data and information generated for project should be placed on web site for scientists and interested parties to access.

CEQA/NEPA compliance and permitting does not require a comprehensive research program. Additional data will be collected to the extent required for a defensible impact assessment. These data will be published as part of the EIR/EIS record in hard copy and electronic form. No use of the web for this purpose is currently planned.

2

2

Long-term monitoring program

Mitigation monitoring and reporting program will be developed as part of EIR/EIS process. The duration of the monitoring program will be developed when project mitigation is identified.

3

3

Peer review process should be used to evaluate research proposals, select scientists to do research, evaluate the conduct of work, evaluate integration of various program elements, and evaluate end products

Peer review will be used in conjunction with reviews by cooperating and responsible agencies of appropriate scopes of work, work progress, and end products.

4

4

BCDC facilitate organizational model and research program to produce information for decision makers

This recommendation was made for BCDC and not the lead agencies responsible for the EIR/EIS. It is outside the scope of NEPA and CEQA compliance

5

5

Evaluate No Action alternative as well as project alternatives; monitor implementation of project

EIR/EIS will evaluate No Action and project alternatives for first year of operation and a future horizon year (e.g., 2015); project mitigation monitoring program will be implemented as a condition of project approval.

6

6

Adaptive management program for the Bay

Unknown whether adaptive management approach to any element of a mitigation monitoring program will be required by regulatory agencies as permit approval condition

Comment Number

Comment Category

Nature of Science Panel Comment

Phase 2 Scope of Work

Recommendations

7

7

Creative solutions for the project

Wide range of alternatives being considered; SFO is currently conducting an international competition for platform design as additional check on conventional design concepts

8

1

Scale of study from local to entire Bay

Local to entire Bay scales to be used in environmental studies as necessary to provide defensible impact assessment

9

2

Temporal scales from tidal cycle to longer than a decade

Impacts will be projected to the first year of operation and a future horizon year (e.g., 2015), for a total of approximately 8 years. Model output from one year will be used as input for the next year to minimize carrying forward small round off errors that produce inaccurate results.

10

Motion and mixing of waters

Model tidal circulation, amplitude, and phasing, residual circulation, and wave field; data collection to fill gaps

This type of modeling and data collection will be done for project studies. Several scientifically acceptable hydrodynamic models are being evaluated for the project including RMA, TRIMM, and MIKE 21.

11

Modeling questions for no action scenario

How will freshwater discharge be affected by global climate change, increased population, and changing economic pressures, particularly those that will alter the ratio of demands for freshwater among urban, agricultural, and environmental uses?

Variability of freshwater influx will be taken into account by assessing a range of past water years from dry to wet. Changes in freshwater influx caused by factors addressed in this question cannot be accurately estimated.

12

How will these changes in the freshwater forcing function affect circulation, mixing, and salinity?

Variability of freshwater influx will be taken into account by assessing a range of past water years from dry to wet.

13

How will the residence time of water in the Bay as a whole and in its sub-systems be altered?

Modeling will be used to compare changes in residence time of water in the Bay between existing conditions and project conditions. Because of the high variability of meteorological, hydrological, and anthropogenic forcing functions in the Bay, it is not possible to accurately estimate long-term future conditions.

Comment Number

Comment Category

Nature of Science Panel Comment

Phase 2 Scope of Work

Recommendations

14

How will the annual flush of South San Francisco Bay be affected?

Modeling will be used to compare changes in annual flush of South San Francisco Bay between existing conditions and project conditions. Because of the high variability of meteorological, hydrological, and anthropogenic forcing functions in the Bay, it is not possible to accurately estimate long-term future conditions.

15

How will changes in residence time affect contaminant levels?

Modeling will be used to compare changes in contaminant levels between existing conditions and project conditions. Because of the high variability of meteorological, hydrological, and anthropogenic forcing functions in the Bay, it is not possible to accurately estimate long-term future conditions.

16

What would be the effects on salinity of any projected changes in the quantity or the salinity of waste treatment plant (i.e., the treatment plants in the South Bay) effluent?

Future quantities of treatment plant effluent are dependent on population growth and future disposal rules and regulations. Projections of treatment plant capacity expansion will be included in the modeling; however, it is not possible to capture changes in discharge limitations which have not yet been formulated by regulatory agencies.

17

Modeling questions for runway alternatives

How will proposed runway expansion strategies alter sediment budgets and change bathymetry and the mix of habitats?

Hydrodynamic and sediment transport modeling will be used to address this question.

18

What will be the effects of future large mitigation projects on flows, flushing, and salinity patterns?

Numerical modeling will be used to evaluate the mitigation plan associated with the proposed project. The design, timing, and extent on other mitigation plans cannot be accurately estimated.

19

How will proposed runway development strategies affect tidal amplitude and phases?

A calibrated hydrodynamic model will be used to address this question.

20

How will proposed runway development strategies affect flood hazards?

Output from hydrodynamic modeling will be used to evaluate changes in flood hazards.

Comment Number

Comment Category

Nature of Science Panel Comment

Phase 2 Scope of Work

Recommendations

21

How will the development strategies affect the wind wave environment and wind-driven transport?

A wind tunnel study will be used to determine impacts of project alternatives on wind. These data coupled with existing information and sediment/hydrologic data collected for the project will be used as input to modeling the wave field near the airport and the wind-wave component of sediment transport.

22

Field studies to address physical uncertainties

Current, temperature, and depth (CTD) and acoustic dopler current profiler (ADCP) data collection for wet seasons

CTD measurements are available throughout Bay. CTD measurements will be made in shallow waters as part of the project. Single point current meters have been deplored in the shallows in September and February. ADCP and tide gauges will be deployed in May/June to assess upwelling conditions and high Delta outflow.

23

Sediment dynamics

What are the contemporary patterns of sedimentation, deposition, and erosion in South Bay?

A calibrated sediment transport model coupled with the results of hydrodynamic modeling will be used to estimate contemporary patterns of sedimentation, deposition, and erosion.

24

To what degree could perturbations of the flow regime by the airport protrusion near San Bruno shoals change deposition and erosion patterns of sediments in South Bay?

Sediment transport modeling coupled with the results of hydrodynamic modeling will be used to estimate contemporary patterns of sedimentation, deposition, and erosion.

25

Are these patterns understood well enough to evaluate the impacts of proposed runway expansions?

Baseline studies are being conducted to gain additional hydrologic and sediment transport data for shallow waters near the airport. These data will provide the inputs necessary to better model sedimentation, deposition, and erosion in the vicinity of the airport.

26

Can we predict sediment input and export rates, and areas and rates of erosion and deposition?

Sediment movement will be estimated with existing mathematical models.

27

Does the configuration of the existing runway still act as an active sediment trap?

This question will be answered by evaluating existing historic data and soil borings that have been made in the area.

Comment Number

Comment Category

Nature of Science Panel Comment

Phase 2 Scope of Work

Recommendations

28

How would different construction scenarios affect the bay-wide sediment budget, and at what scales?

Numerical modeling will be used to evaluate the identified construction scenarios for each project alternative.

29

How would different construction scenarios affect wetlands in different areas of the Bay?

Sediment transport will be modeled and estimates of the extent of transport will be used to determine if sediment will travel to the margins of wetland areas.

30

Will the quantity and quality of sediment available for marsh restoration, and/or sedimentation in harbors, change with changes in water movement, erosion of previously deposited sediments, and sediment transport?

This question will be answered using hydrodynamic and sediment transport modeling.

31

The panel recommends an examination of the area around SFO influenced by existing runways using hydrographic charts and cores to estimate the extent of the shadow area of sedimentation and the rates of sedimentation that is caused by the present runway configuration

The historic hydrographic charts of the project area will be reviewed for correlation with model results. Calibrated hydrodynamic and sediment transport models will be used; therefore, additional cores to estimate sedimentation rates are not necessary.

32

What are the sedimentological effects of the proposed projects within the context of changes that have already taken place and that could take place?

Calibrated hydrodynamic and sediment transport models will be used to evaluate the project and project-related mitigation. Cumulative impacts of other planned projects having a major effect on Bay sediments will be addressed.

33

Runway construction

How could negative impacts be reduced through selection of fill material and engineering strategies?

SFO is currently conducting an international competition for platform design is underway as an additional check on conventional design concepts. If fill is used for platform construction it will meet DMMO requirements for sediment chemistry as well as appropriate engineering design characteristics.

34

How much sediment is "lost" in the dredging-disposal-fill operations, what are the impacts, and how could the losses be reduced to a minimum?

Sediment loss will be addressed in the evaluation of borrow site and runway construction design. The impacts of this action will be evaluated using hydrodynamic and sediment transport models.

Comment Number

Comment Category

Nature of Science Panel Comment

Phase 2 Scope of Work

Recommendations

35

Borrow Areas

Would proposed runways or borrow areas create large sediment sinks?

This question will be answered with calibrated hydrodynamic and sediment transport models. Baseline data on currents and bathymetry at potential borrow sites will be collected to provide input to the models.

36

Where will the fill come from? What will be the effects at the borrow sites of different excavation strategies?

Four borrow sites in the Bay Area and two outside of California are being considered for the project. Engineering and environmental analysis will be used to determine the appropriate method of dredging.

37

How much sediment is lost during dredging and transport?

Sediment loss will be calculated in the design of the dredging operation.

38

What are the impacts of borrow areas on circulation?

A calibrated hydrodynamic model will be used to address this question.

39

Potential changes in contaminant distributions and effects

Because annual flushing appears to be very important in removing contaminants that build up in South Bay, to what degree would the location of the protrusion of new runways increase the potential for affecting the annual flushing?

A calibrated hydrodynamic model will be used to address this question.

40

How might the changed circulation patterns uncover the historic contamination legacy or otherwise change the contamination level of the suspended particulate load in South Bay by remobilizing contaminated sediments?

Hydrodynamic and sediment transport modeling will be used to address this question.

41

Will any change in sediment structure near the new runways change the patterns of bioaccumulation of contaminants?

Potential changes in bioaccumulation will be estimated based on the results of sediment characterization, hydrodynamic and sediment transport modeling results, information on organisms in the area affected, and published literature on bioaccumulation. However, it may not be possible to evaluate change in bioaccumulation patterns because of the lack of detailed information on bioaccumulation in the Bay.

Comment Number

Comment Category

Nature of Science Panel Comment

Phase 2 Scope of Work

Recommendations

42

How will various construction scenarios affect the availability, fate, and effects of contaminants?

Dispersion of contaminants during dredging and placing of fill will be evaluated by numerical modeling using inputs from sediment testing in accordance with DMMO requirements.

43

How will changes in water residence time affect contaminant levels?

Water quality modeling using the results of hydrodynamic modeling will be used to address this question.

44

How much contamination is mobilized during dredging, disposal, and filling?

Dispersion of contaminants during dredging, dredge disposal, and placement of fill will be evaluated by numerical modeling using inputs from sediment testing in accordance with DMMO requirements.

45

How can the releases be minimized?

Methods to minimize contaminant mobilization will be evaluated following estimation of the nature and severity of the potential problem.

46

How much of the borrowed sediment for runway construction is contaminated?

This question will be addressed through sediment characterization in accordance with DMMO requirements.

47

How does the quality of fill material affect leaching rates of contaminants, their sorption onto sediments, their release, and resulting impacts?

This question will be addressed through sediment characterization in accordance with DMMO requirements.

48

To what degree are air emissions from tugs and earth-moving machinery during dredging and disposal a concern?

Air emissions associated with construction will be characterized and their conformity with the State Implementation Plan will be evaluated.

49

Sampling programs are recommended to examine contaminants in water, sediments, and biota.

Published literature and sediment sampling and analysis will be used characterize baseline contaminant concentrations in sediments. Published literature will be used to characterize contaminants in water and biota.

Comment Number

Comment Category

Nature of Science Panel Comment

Phase 2 Scope of Work

Recommendations

50

Potential biological impacts

How might regional or larger scale changes in circulation, turbidity, sedimentation, bathymetry, water quality, and /or contaminant levels, contribute to changes in ecosystem function such as patterns and rate of phytoplankton production?

Hydrodynamic, sediment transport, and water quality modeling results together with fish and benthic surveys of the project area and existing biological data (such as the 19 years of data from California Department of Fish and Game) will be used as input to assess biological impacts including ecosystem functions.

51

Do changes in bathymetry on the west side of the Bay affect uses of that area, as well as the estuary as a whole, by fish and wildlife?

Hydrodynamic, sediment transport, and water quality modeling results together with fish and benthic surveys of the project area and existing biological data for the Bay will be used to address this question.

52

If there is a change in the mix of habitats, are the changes significant biologically? How would resultant biological alterations be manifested?

Hydrodynamic, sediment transport, and water quality modeling results together with fish and benthic surveys of the project area and existing biological data for the Bay will be used to address these questions.

53

What are the effects on fish and wildlife resources from the disturbance, displacement, and release of sediments and contaminants during and following runway construction?

This question will be addressed based on water quality modeling using sediment characterization data, existing data, project-specific surveys on fish and wildlife, existing data on fish and wildlife resources of the Bay, and published toxicity data.

54

Eelgrass near the Oakland Airport represents a unique community in San Francisco Bay. How will construction of new runways at Oakland affect present eelgrass beds and the fish and wildlife dependent on them?

The EIR/EIS will address cumulative impacts of potential development of Oakland Airport.

55

If there are changes in patterns of sediment erosion and accretion or in the tidal amplitude which alter the structure of tidal wetlands and adjacent intertidal mudflats, what are the impacts on the fish and wildlife resources dependent upon these areas?

Hydrodynamic, sediment transport, and water quality modeling results together with fish and benthic surveys of the project area and existing biological data for the Bay will be used to address these questions.

Comment Number

Comment Category

Nature of Science Panel Comment

Phase 2 Scope of Work

Recommendations

56

What will be the effect on wildlife from increased noise?

Existing literature on the impact of noise to wildlife will be used to address this question.

57

Effects on birds

What would be the effect of these displacements on resident and migratory bird populations?

Existing information on waterfowl and shorebirds collected by SFO and bird surveys done for the project will be used to address this question.

58

Because birds tend to have high site fidelity, what is the potential for increased conflicts between birds and airplanes? For instance, will such conflicts affect the endangered least tern?

Existing information on waterfowl and shorebirds collected by SFO and bird surveys done for the project will be used to address this question.

59

Which birds would be favored by the construction and the resulting changes in bathymetry and sediment texture — shorebirds or diving waterfowl?

Hydrodynamic, sediment transport, and water quality modeling results together with sediment characterization, bird surveys conducted for the project, and existing data will be used to address this question.

60

How would runway construction alter bird food supply? What would be the effects?

Fish and benthic surveys of the project area and existing literature will be used to address this question.

61

Is it possible to mitigate loss of shallow, sub-tidal habitat? How? What are the effects?

Project mitigation investigations will explore opportunities for mitigating loss of shallow, sub-tidal habitat.

62

Scoter, in particular, are abundant at the airport sites in winter and constitute an important water use. Comparative studies should be carried out to assess the relative importance of these areas to the scoter population.

Surveys of diving ducks in the project area will be conducted to assess potential impacts of project alternatives. Scoters winter in many areas of the Bay. Existing data on these other habitats will be evaluated along with information on the characteristics of the habitat in the project area to assess potential project impacts to this species.

63

How has the loss of habitat affected these species in similar situations elsewhere?

Existing published information and data from resource management agencies will be reviewed to address this question.

64

Will change in sediment structure adjacent to new runways change the foraging potential of the region?

Hydrodynamic and sediment transport modeling results as well as fish and benthic surveys of the project area will be used to address this question.

65

Effects on fish

Existing data should be evaluated to assess the importance of the proposed fill areas to important fish species.

Existing published information and data from resource management agencies will be used to assess potential impacts of project alternatives.

Comment Number

Comment Category

Nature of Science Panel Comment

Phase 2 Scope of Work

Recommendations

66

What are the existing uses of the proposed runway fill areas by herring, surf perch, California halibut, sharks, and other species of the area? How would 2-4 mi² of fill, and the conversion of subtidal areas to intertidal areas as a result of sedimentation, affect their populations?

. Hydrodynamic, sediment transport, and water quality modeling results together with fish and benthic surveys of the project area and existing biological data for the Bay will be used to address these questions

67

What are the patterns of temporal and spatial abundance and community structure in fishes of western South Bay? Larval and young stages have the strongest correlation to currents and salinity.

Fish and benthic surveys conducted for the project and existing data collected by resource management agencies will be used to address this question.

68

What is the recreational fishery in the areas that would be impacted by expansion of the airport runways and how would these areas be impacted under different scenarios?

Fish and benthic surveys conducted for the project and existing data collected by resource management agencies will be used to address this question.

69

Pacific herring and surf perches

Assess relative importance of project area

Fish and benthic surveys conducted for the project will be used to address this question.

70

Salmon and steelhead

Assess use of project site by salmon and steelhead; tissue retention of chinook salmon tissue for subsequent DNA testing.

Fish surveys conducted for the project will be used to address this question. If chinook salmon are collected, tissue samples will be collected and retained for subsequent analysis.

71

Effects on mammals

Will hydrodynamic changes affect erosion rates of tidal marsh, especially near haulouts on the west side of the South Bay?

Hydrodynamic and sediment transport modeling results to be used to address this question.

72

Will mudflat topography be altered in the vicinity of the seven South Bay haulout sites, affecting overall access and the tidal range when the site is available to seals?

Hydrodynamic and sediment transport modeling results to be used to address this question.

Comment Number

Comment Category

Nature of Science Panel Comment

Phase 2 Scope of Work

Recommendations

73

Will runway expansion alter airplane landing patterns over the Bay, increasing noise levels and/or disturbance at the three haulout sites near Redwood Creek and at the haulout on Yerba Buena Island?

Noise modeling results and existing information on noise impacts to wildlife will be used to address this question.

74

Will on-site runway construction or more distant support activities disturb hauled seals and/or alter pupping activity?

Hydrodynamic, sediment transport, and water quality modeling results together with fish and benthic surveys of the project area will be used to address this question.

75

What effect will any disturbance or haulout site loss have on haulout site use, pup mortality, seal numbers, or overall seal activity within the Bay?

Hydrodynamic, sediment transport, and water quality modeling results together with fish and benthic surveys of the project area will be used to address this question.

76

Prey Availability

Will changes in fish recruitment or species composition affect seal prey availability?

Fish and benthic surveys conducted for the project will be used to address this question.

77

Will seal foraging areas be affected by construction related hydrodynamic changes?

Hydrodynamic, sediment transport, and water quality modeling results together with fish and benthic surveys of the project area will be used to address this question.

78

If prey availability or access is reduced, will it alter seal numbers or activity within the Bay?

Hydrodynamic, sediment transport, and water quality modeling results together with fish and benthic surveys of the project area will be used to address this question.

79

Contaminants

Will toxic residues increase in the Bay’s harbor seals and in their prey? What effect will a further increase have on seal health and behavior?

Water quality and sediment transport modeling results and existing information on toxicity will be used to address this question.

80

Effects on South Bay marshes

A field program needs to be carried out in combination with new modeling to help quantify the potential impacts of project alternatives on South Bay marshes.

Hydrodynamic and sediment transport modeling will provide information at the interface of the Bay and marshes. If this information indicates a potential impact, the need for further analysis will be evaluated.

81

What are the existing rates and locations of marsh aggradation and erosion and the associated sediment supply and hydrodynamic regimes?

This question will be addressed for specific mitigation sites in the design of the mitigation plan.

Comment Number

Comment Category

Nature of Science Panel Comment

Phase 2 Scope of Work

Recommendations

82

What are the salinity patterns in the water column and in the soils?

This question will be addressed for specific mitigation sites in the design of the mitigation plan.

83

What is the present distribution of plant communities?

Biological surveys will be conducted for specific mitigation sites during the design of the mitigation plan.

84

What are the patterns of tidal amplitudes in the open bays and within tidal marsh channels large and small?

Hydrodynamic modeling will be used to addressthe question of tidal amplitudes in the Bay. If this information indicates a potential impact in marshes, the need for further analysis will be evaluated.

85

What is the present distribution of non-indigenous plant and animal species?

Existing information will be used to address this question if it is relevant to the project impact assessment.

86

What is the best forecast of the ecological processes and consequences of non-indigenous species recruitment and population growth?

Existing information will be used to address this question if it is relevant to the project impact assessment.

87

Will increased mudflat area around airports be sites for accretion of exotic marsh plants?

Hydrodynamic and sediment transport modeling results will be used to estimate any increase in mudflat area. Existing information on habitat requirements of exotic marsh plants will be used to evaluate the potential for accretion of these plants.

88

Effects of wetland mitigation

What are the biological effects of building large number of wetlands in a short period?

Hydrodynamic modeling results, existing biological information, and biological surveys of mitigation sites to be included in the mitigation plan will be used to address this question.

89

What is the potential for invasive species to become dominant in new wetlands?

Existing literature will be used to address this question. The mitigation plan will include monitoring for abundance of invasive species and corrective actions if this becomes a problem.

90

Will there be significant changes in tidal prism as a result of opening large areas of diked baylands to tidal action? If so, what might be the effects?

Hydrodynamic modeling results that include the proposed habitat mitigation plan will be used to address this question.

91

How would different mitigation strategies affect residence time of water in South Bay?

Hydrodynamic modeling results that include the proposed habitat mitigation plan will be used to address this question.

Comment Number

Comment Category

Nature of Science Panel Comment

Phase 2 Scope of Work

Recommendations

92

How do mitigation strategies affect sediment dynamics, especially within and adjacent to marshes?

Hydrodynamic and sediment transport modeling results that include the proposed habitat mitigation plan will be used to address this question.

93

What are the site-specific impacts of the mitigation measures, such as adjacent levee stability, flood hazards, utility corridor access, changes in mudflat availability for shorebirds, recreational use, etc?

Impacts of the habitat mitigation plan will be addressed in environmental studies for the EIR/EIS.