Its unlikely they'll join right away, the CSA might send an expedition. Some SC politicians might consider it, and a few Californio hopefuls maybe even their own secession. Slavery or not, in a separate SC the land-owningCalifornio families will have a bit more sway and political power than in the larger California of OTL.
Water would not be an issue just yet. Water rights became an issue as LA exploded in the early 1900s. Even now most of the water comes from the Colorado River. And just like that watershed is shared with Arizona, Nevada, Utah, Colorado, and Mexico the Owen's Valley source will have to be negotiated with North California. Most of the water was used to irrigate the San Fernando and San Bernardino Valleys; assume less development in these areas, and greater development around Ventura County and the Owen's Vaitselfstelf (which might keep some of its water).
SC can still grow, the area has a lot to offer. Remember LA was an oil town and manufacturing hub first and foremost. The coastal counties are great for agriculture. Both San Pedro and San Diego have great inlets on which to build ports on. Like in OTL, it's just a matter of time for a railroad to cross from the Gulf to Southern California. And the weather will always be great to attract immigration. Water or no water SC will figure it out just like Pheonix figured it can pump water to a desert plateau where there shouldn't be enough water to sustain a city its size; yet... there it is.