
In the Summer prevailing winds from the Northwest are generated by a large, high pressure area several hundred miles off the California coast. The outward, radial movement of air from the high is twisted into a clockwise spiral by the rotation of the earth (Coriolis force). The force of the surface winds augment a giant ocean gyre, the Japanese current, to drive surface water South along the coast.
Winter Winds in Sausalito by Shirwin Smith: Feb 06 OWRC News Letter
A great little book: Weather of the San Francisco Bay Region by Harold Gilliam
Sailing the Bay by Kimball Livingston. Maybe less comprehensive on weather than Gilliam's book, but has information on tides, currents, waves and history of the Bay. I give it a slight edge.
Real time wind and water:
webcam on Sausalito beach (South end) looking toward San Francisco;
webcam at Sausalito Yacht Club;
webcam at Richardson Bay Audubon Center;
webcam at Ayala Cove, looking out over Raccoon Strait;
wind, water, and webcam at the Romberg-Tiberon Lab;
wind conditons at the Golden Gate and other Bay locations (NOAA).
ocean swells outside the Golden Gate

Up-welling generates a 10-100 mile wide band of cold water, rich in minerals, feeding green plankton that are at the bottom of the food chain. In the past these plankton have provided the Bay Area with a generous harvest of seafood. Unfortunately, overfishing and pollution has greatly reduced that bounty.
Fog
The prevailing wind blowing over warm surface water of the Pacific picks up a lot of moisture before it hits the band of cold water along the coast. A temperature inversion is then created, with cold, heavy air on the bottom of warmer upper air (the inverse of normal). If air on the surface cools below the dew point we have fog. If the wind is mild the fog stays on the water, prevented from getting to Sausalito and the East Bay by the costal range of hills. If the wind is moderate, the fog blows through the Golden Gate. If the wind is stronger, the fog blows up over the costal hills and down into the Bay.
In summer the major engine transporting fog into the interior is hot air rising from the Central Valley. The air along the coast is drawn to the East to replace this rising hot air. Thus, the Westerly winds are usually strongest in the afternoons when the land is warmest, and don't effect rowing in the early morning.
Animation of the summer fog cycle
If you see fog blowing through the Golden Gate, or over the Sausalito hills, there has to be wind somewhere. If you are planning to row outside Richardson Bay fog coming through the Golden Gate is a warning.

Winter
In between storms the winds are usually quite mild. This can be the best season for rowing, even though sailors don't like it. However, occasionally we have a Northerly breeze that can start early in the morning (it's not generated by a hot interior). Since the wind is blowing toward the OWRC the chop is bad once you leave the dock. It can actually be the worst near shore, since the waves reflect from the docks generating a vicious combination of wave fronts.
A common way to escape the chop is to go up into the Strawberry area. A similar strategy is to row into the wind shadow of the Belvedere peninsula However, if you escape to a sheltered region and play around for a half hour or so, the wind can increase, and when you decide to return to the OWRC you can be in for an unpleasant surprise. While the Northerly breeze usually decreases as the day progresses, it sometimes gets stronger. The good news is that on the return to the OWRC you will be rowing with the wind and waves. Anyone for surfing?
If you leave the OWRC and go along the shore toward the center of Sausalito it can be an easier row, since you are rowing partially down wind. However, getting back is going to be a lot more work. There are few free lunches.

The current along the coast is weaker, and the up-welling less than in the Summer.