A federal order went into effect Nov. 1 governing the spraying of mosquito pesticides under the Clean Water Act.
The rule would bar seasonal fogging by vector control agencies near waterways deemed impaired by the federal government.
Officials say mosquitoes have risen early from their hibernation, and worry that a late rain could provide a West Nile breeding ground.
"We could definitely see an increase in the number of human cases of West Nile virus," Dr. Steve Schutz, scientific program manager of the Contra Costa Mosquito & Vector Control, said.
Vector control agencies also worry the new rules could hamper efforts to control the invasive Asian tiger mosquito, found in Santa Clara county six years ago and quickly quarantined. That pest is known to carry dengue fever as well as West Nile.
Eight people died in the state in 2011 from West Nile out of 155 cases reported, according to the California Department of Public Health.
In general, people bitten by a mosquito carrying West Nile show no symptoms. Officials say about 20 to 30 percent of people bitten will get the disease's flulike symptoms, and less than one percent suffers from a brain inflammation.
Environmental groups applauded the new rules, saying there are non-toxic methods for battling mosquitoes.
Scientists from California's 65 vector control agencies will be discussing the new rules at a meeting Monday and Tuesday in Burlingame.
A bill that would exempt vector control agencies from the regulations has passed the U.S. House of Representatives and is awaiting action in the Senate.