How would one be able to drill a water well in the county area of
California City when the deed states "excepting all water in and under
said land and the water rights appurtenant thereto."

"This deed is made and accepted upon the covenants and conditions set
forth in the protective covenants recorded in book 3933, page 373" 
This is in Kern County, California.  My 20 acre parcel of land (
Parcel 13 on Parcel Map 3 filed in Book 1, pages 1 to 12 inclusive of
parcel maps)  has recently been "detached" from the City of California
City and now falls under jurisdiction of Kern County.  After 40 years
of ownership, I'd like to build something on it but need water and
don't know where to start the process.  Does anyone have any knowledge
in this area?  Thank you.

HI, this is kind of disjointed, sorry.
I'd go to the county and ask.  Maybe the exception of the water rights
only applied as a condition for property in City of California to
avoid wells within the city limits and force people to hook up to the
water system.
That would be almost too good.
But if that were the case, then it is a question of whether you would
have to have the condition removed or if it is simply no longer
applicable.  (Please see the disclaimer below concerning profession
advice.  This is not such.)
I wouldn't press the question too hard with the county, just ask what
the exception means and hear what they say.  They could decide that it
was a nice idea that you didn't have water rights and want to keep it
that way.
Oh, better, start in City of Cal., which no longer is responsible and
won't mind hearing that you'd like to put in a well.
And, of course, you can ask an experienced real estate agent.  He or
she will tell you all he/she knows if it seems like you are
considering selling the parcel and they got to list it.  And they
would/will tell you that clarification of the point is very important
if you did want to sell.
I'd do that first, easy, no cost, and maybe you'd get some other
useful info from the conversation.  Could talk to a couple to hear if
they agree.
Good Luck

Thank you myoarin-ga for the good tips.  I will get started right away
as I know the process will be lengthy.  Didn't think about asking a
real estate person.  Thanks again!

My pleasure, good luck!