The Sacramento River and nearshore ocean areas will get more slime and goo from the city streets flowing into the sea, but the Sacramento river and all rivers from the mountains in California are bringing lots of silt, debris, and nitrogen wastes additionally. Most of the "muddy" color is due to silt during the rainy season, as is with any river. I've worked at a Sonoma County beach for the last 7 years and have followed water quality as well as looked at some data regarding water quality over the last couple of decades. In Sonoma County, the beaches have tested with higher levels of bacteria in recent years, but places like Campbell Cove in Bodega Bay, are almost always testing with lousy water quality. Be especially careful with open sores, cuts and wounds being exposed to dirty beach water and sand. Your chances of testing positive for MRSA on your next hospital visit increase dramatically. Many of us are colonizing this stuff on our skin as it is...but a healthy immune system keeps it in check.
Another problem with water quality up North is the dramatic increase in runoff from Northern California vitniculture, and dairy farm runoff. Some researchers are suspecting the jellyfish blooms are a result from this nitrogen that in turn causes the algae blooms that were responsible for the severe red tides that killed off many of the nearshore critters this year including abalone.
Having been told all of this, I'm still a huge fan of diving these waters and as long as I'm healthy, not swallowing large amounts of seawater, and portals of entry in my body are protected, I feel safe diving. If you are severely immunocompromised, dive with caution.
I dove Lover's on a rainy day and it was Awesome! Depending on how hard the rain is, there may be murky water close to where the runoff is coming in, but otherwise other swell, wave and current data will probably affect visibility much more, and the deeper, less sandy areas will not be affected at all.