Steer clear of the chocalate water (runoff) near shore. Most of the typical offshore dive sites (1-2 miles) range from 8-12 ft to 15-20 ft. Deeper sites like wreck alley are more variable. The real issue is the real strong southwest swells, they can really churn up the water at any depth usually dictated by what is on the bottom (rocks, mounts, sand, etc). We just had two days of torrential downpours. But I find that the dive conditions in these rains (for the last two months) seem to be more dictated by the swells/currents.
On the other hand, I am logging buko dives right now and loving it. Boning up on uw nav, and really getting to know the sites. You know the viz is never all that great here anyway. If you haven't been in kelp, that'll be worth it.
Lots of shore diving and plenty of boat diving out of Mission Bay / Quivera Basin area