Roger Reynolds Nursery is at 133 Encinal Ave. in Menlo Park.
Ms. Weiler, 31, is a resident of Fremont and has been employed at the nursery since October 2008, police said. She was booked into the San Mateo County jail.
The case unfolded after a routine audit of the nursery's books in January showed steady declines in account balances, police said.
Auditors then discovered "dozens of checks" written to Ms. Weiler and a Fremont accounting business called "When Every Penny Counts," police said.
Menlo Park Police Office Jeff Keegan conducted an extensive investigation before seeking a $250,000 warrant for Ms. Weiler's arrest, Sgt. Dixon said.
Police are asking anyone with information on the case to call Office Keegan at 330-6300 or the anonymous tip line at 330-6395.