Bay Plan Map 5 Identifies a seal haul out location at the southern shore of Alameda and directs the commission to "Protect Harbor Seal Hault-Out and pupping site where harbor seals rest, give birth, and nurse their young. Projects allowed only if protective of harbor seals and other sensitive wildlife."
This is about dealing with areas of particular concern for trash pollution.
The workflow with Fremont shoreline is special. You must take into account the potential for Eelgrass bed impacts.
I recommend that you examine the attached document. Determine whether the attached provisions are relevant. Then consult the available data for the eelgrass beds, provided by NOAA.