SAN MARCOS — City leaders are cracking down to make sure rain doesn’t spread pollution, but the mayor says the city needs more money to do it.

The San Marcos City Council unanimously but grudgingly approved modifications to the city’s storm water handling procedure March 11. The new Storm Water Standards Manual incorporates the provisions of the latest permit issued by the Regional Water Quality Control Board.

Every time it rains, storm water runs downhill from city and county properties. This water, if left untreated, transports artificial and biological contaminants into streams, reservoirs and the ocean.

Storm water is an intermittent and highly local problem, so the Environmental Protection Agency has delegated its Clean Water Act powers to California’s State Water Resources Control Board, which then regulates the state’s storm water transport and handling practices through the various Regional Water Quality Control Boards.

Federal law requires that the state issue a new Municipal Storm Water Permit every five years, the most recent of which was adopted by the San Diego Regional Water Quality Control Board in January 2007.

“No matter what condition the water is when it gets to our property, when it leaves our property, it’s supposed to be pure water,” City Attorney Helen Holmes Peak said of the new permit requirements at the meeting.

“The significant difference between the 2001 and 2007 storm water orders is the amount of follow-up and follow-through that is required of the (cities),” Public Works Director Mike Mercereau explained after the meeting.

Under the original plan, cities were required to have a program that regulated how businesses and residents controlled their storm water. Under the 2007 plan, cities are now obligated to inspect each site proactively.

The implementation and enforcement of the requirements of the new permit will generate new costs. Changes to the San Marcos Storm Water Manual include the ability to impose additional fees upon customers in order to recover the costs of establishing and monitoring the storm water discharge pollution control system.

The city is expected to pick up the tab for the expanded storm water oversight — an expense that will range from several hundred thousand dollars to more than $1 million, according to Peak.

According to Peak, many of the requirements of the new state permit go beyond what the federal government requires under the Clean Water Act. While the city has to bear the burden of the federal orders without external funding, this is not true of state dictates.

San Marcos is currently pursuing a joint unfunded mandate legal action along with other cities in the county against the state of California to recover some of the costs incurred under the new permit, but this promises to be a long and uphill battle.

“I don’t know. I’m all for green and sending off clean water, but it seems these are onerous mandates ... we’re regulating ourselves out of work and out of money,” Mayor Jim Desmond said at the meeting.