Those are the salt ponds - Cargill(they may have sold them?) brings in water from the bay, evaporate it, and harvest the salt. Evaporating seawater and the various algae/bacteria in the flats create bad smells.

Why does Union City smell bad?

UNION CITY — Something is stinking up the air around the Union Sanitary District sewage treatment plant. ... In recent years, Union Sanitary, sandwiched between the shoreline and housing developments west of Union City Boulevard, has attributed foul smells to the Bay.

Why does Newark CA smell bad?

An unpleasant smell around Newark is lingering and the source of the odour — described by residents as a mix between sewage, cannabis, vomit or sugar beet — is an ongoing mystery. ... The stench, however, has been reported by residents to be present from as far as Coddington, Collingham and Brough.