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Years ago, I did some fisheries survey work in the Bay/Delta region; mostly on a 42' trawler. We sampled from Big Break and Rio Vista, downstream throughout the rest of the Delta and Bay.
A few points to think about (that may all be obvious, anyway):
- this time of year it's often easier to make such a trip than it is during the summer (those afternoon Delta "breezes" can make westward progress almost impossible);
- if you do get a stiff west wind, you might as well find a harbor (or anchor in a side slough) -- if there's an ebb tide set against the wind, the steep wave faces will pound the Bejeezus out of you and your boat -- if you have a flood tide working with the wind, you probably won't make any progress anyway;
- there are plenty of hide-e-holes in side sloughs, behind little islands, et cetera; take a good anchor and a rode with a couple of boat lengths of chain, in case you have to wait out any bad weather;
- the bottom is ever-changing, DON'T trust your charts in areas with any hint of shoaling -- particularly the area around the Sacramento/San Joaquin convergence (but, really anywhere);
- Once you get down into the Bay (below Vallejo), the tide shouldn't be nearly the problem that it is in the Delta/Suisun Bay/Carquinez Straight; between Antioch and Mare Island is the area you'll have to deal with tides the most (basically, that part of the trip where you'll be using the Suisun Bay chart).