Under new ownership the San Pablo Yacht Harbor has become a friendly sea kayaking destination. Easy access to East Brother Islands from here. If tides are favorable you can also paddle to Red Rock Island from here.
Great brace practicing for currents and eddies to be found around the East Brother Islands. You can ride the ebb and flood and countercurrents around the islands many times here. Beware of the Vallejo ferry and tugboats which can go around Point San Pablo very fast.
Disclaimer
These are put-ins that I have used, and maybe totally different when you are there, in other words, paddle at your own risk.
Always check weather and ocean conditions before you paddle!
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