Lower  South  Bay  (LSB),  a  shallow  subembayment  of  San  Francisco  Bay  (SFB),  is  situated  south  of   the  Dumbarton  Bridge,  and  is  surrounded  by,  and  interconnected  with,  a  network  of  sloughs,   marshes,  and  former  salt  ponds  undergoing  restoration (Figure  ES.1).  LSB  receives  120  million   gallons  per  day  of  treated  wastewater  effluent  from  three  publicly  owned  treatment  works   (POTWs)  that  service  San  Jose  and  the   densely  populated  surrounding  region.   During  the  dry  season,  when  flows  from   creeks  and  streams  are  at  their   minimum,  POTW  effluent  comprises  the   majority  of  freshwater  flow  to  Lower South  Bay.  Although  LSB  has  a  large   tidal  prism,  it  experiences  limited  net   exchange  with  the  surrounding  Bay,   because  much  of  the  water  that  leaves   on  ebb  tides  returns  during  the   subsequent  flood  tides.  The  limited   exchange  leads  to  distinctly  different biogeochemical  conditions  in  LSB   compared  to  other  SFB   subembayments,  including  LSB  having   the  highest  nutrient  concentrations  and   highest  phytoplankton  biomass.   

This  report  was  prepared  as  one  in  a  series  of  reports  that  explore  the  current  state  of   knowledge  on  nutrient-­‐related  issues  in San  Francisco  Bay,  in  support  of  the  San  Francisco  Bay   Nutrient  Management  Strategy (NMS).  The  report’s  main  goals  are:   

• Synthesize  data  and  observations  in  LSB  related  to  nutrient  inputs  and  cycling  in  LSB,   major  indicators  of  ecosystem  response  to  nutrients,  and  the  range  of  physical,   chemical,  and  biological  factors  that  regulate  ecosystem  response;
• Identify  major  data  or  conceptual  gaps  across.   

The  report  is  organized  as  follows:

• Section  2:  Nutrients:  loads,  seasonal,  spatial,  and  ambient  concentrations,  and  evidence   for  the  importance  of  in  situ  biogeochemical  transformations  (Section  2)
• Section  3:  Suspended  sediment  concentrations,  and  their  influence  on  light  levels 
• Section  4:  Abundance  of  benthic  grazers
• Section  5:  Phytoplankton  biomass
• Section  6:  Dissolved  oxygen  concentrations
• Section  7:  Fish  abundance 
• Section  8:  Priority  science  questions,  and  proposed  activities  to  address  those  questions.