The decision came after a determination by county lawyers that he can't.
Navarro, a school board member since 2006, was elected in a November to a seat on the water board that he took Jan. 8.
In December, County Counsel Jean-Rene Basle drew from a previous attorney general's opinion that representing a water district and school district could lead to a "significant clash of duties and loyalties," for instance because the water district sets wholesale prices that retail water agencies then pass on to school districts.
Even a potential future significant clash means the first office must be resigned, according to the attorney general's website.
But the school board voted 4-0 on Monday - with Navarro abstaining - to ask the attorney general whether the offices were compatible.
"This is a legal matter that needs to be resolved, and the proper channel is to go through the attorney general," board President Bette Harrison said in a statement from the county superintendent's office.
Navarro said he supported that decision, although he expected a backlog of cases in the Attorney General's Office would mean it would take a year and a half to get an
"I have no problem with the process other than it's a waste of taxpayer dollars," Navarro said.
Navarro's school board seat, which represents schools in San Bernardino and Rialto, is up for election in November 2014.
Navarro's school board pay was $18,369 for the 2011-12 year, including health and welfare, according to county schools spokeswoman Christine McGrew.
The water district pay is $385 per day, with a 10-day limit for each month, according to general manager Doug Headrick.
This report has been corrected to indicate the vote was 4-0, with Navarro abstaining.