@Annie1 Russian River...I have done parts of this in a canoe and parts in an inflatable Kayak...there were a number of portages on the kayak trip I did and a few very minor shallow "rapids".
Tomales bay from Hearts Desire beach. It's quite calm, warm, shallow and protected around the beach but Tomales bay can be very windy particularly in the afternoon so make sure you know what you are doing. I have not kayaked there. In the winter you can see bioluminescence in Tomales bay. I believe bluewaterskayaking have kayak tours to see it though generally they rent boats.
Lake Sonoma has boat in camp sites. I think one arm of it is restricted from ski boats but I'm not sure. https://www.paddlingcalifornia.com/Lake_Sonoma.html
Lake Berryessa has various arms that are not really accessible to motor boats. https://www.usbr.gov/mp/ccao/berryessa/docs/paddling.pdf
Haven't been there in a long time but kayaking around the marinas and houseboats in Sausalito might be of interest. It's the bay so be careful.
When there is baseball McCovey cove is popular ...