The groundwater basins supply much of the Inland Empire region.
The U.S. Geological Survey says nitrate usually comes from agriculture and wastewater treatment operations. Perchlorate can come from rocket fuel, fireworks and fertilizers.
Both substances appeared in the Upper Santa Ana Valley and the San Jacinto groundwater basin.
According to the Press-Enterprise, local officials weren't surprised by the findings and already treat the water for contaminants.
The project is evaluating more than 120 groundwater basins statewide for things such as pesticides and solvents. Nitrate from agricultural activity was found in 25 percent of the study area, and high concentrations of perchlorate were found in 11 percent of the study area.
The Associated Press contributed to this report.