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In August 2003, the North County Transit District, preparing to build a train line linking Oceanside, Vista, San Marcos, and Escondido, applied to state authorities for a storm water discharge permit. The train, called the Sprinter, would run along a 22-mile stretch of old freight line that parallels Loma Alta Creek through much of Oceanside and crosses several streams. Parts of the rail bed would require improvement, new track would have to be laid down, and 15 stations and 5 bridges would need to be built.

Compliance with clean water laws requires preventing erosion at construction sites. Unless graded dirt is controlled — held in place by fiber or vegetation — rainfall washes it down storm drains and into creeks. Satisfied that the transit district would comply with clean water laws, the local branch of the state water quality authority, the San Diego Regional Water Quality Control Board, issued a permit for the construction.

Three years later, as the line was being built, transit officials held a party to give the public its first look at the train. Emerging from a railroad barn to the theme music from the movie Rocky, a Sprinter car made a debut run of 150 feet. The sleek blue-and-turquoise car stopped and parked long enough for the crowd to admire it and to hear transit district executive director Karen King hail it as “truly unlike any train you’ve seen before.”

Built by Siemens Transportation Systems in Germany, the Sprinter needs no locomotive. It is propelled by two 420-horsepower diesel engines installed under the car’s floor. At 135 feet long, it seats 136 passengers and has room for another 90 standees. On each end is a blunt fiberglass nose cone that will cut through North County at speeds of up to 55 miles an hour. Each car costs more than $4 million. An ever-escalating price tag for the new line has brought the overall cost from $352 million in 2003 to an estimated $478 million now — more than $21 million per mile.

Meanwhile, citizens in Oceanside and San Marcos were complaining to the water quality control board that when it rained, pollutant-laden dirt was washing off Sprinter construction sites and into creeks and a lake.

On February 20, 2007, the board sent Ben Neill, a state water resource control engineer, out to take a look. It had rained more than a third of an inch the day before, according to the National Weather Service’s station in Vista, a “not extraordinary amount,” Neill would write in a report.

The engineer found dirt flowing into municipal storm water systems and “navigable waters of the United States” at nine separate locations in Vista and San Marcos.

The report listed two sites in Vista — one east of Escondido Avenue and the other at the Sprinter’s storage yard near Mar Vista Drive — that sent sediment into the Buena Vista Creek, which flows into the Buena Vista Lagoon. In San Marcos, the report catalogued “discharges” going into San Marcos Creek at seven different locations; six of them near the civic center and Cal State San Marcos along Barham Lane and Shelly Drive and the seventh in the ArmorLite storage yard near the Sprinter station that will serve Palomar College. San Marcos Creek ends up in Lake San Marcos, a scenic and recreational gem of the community.

As a result of the inspection, the water quality board on March 19 issued the North County Transit District a notice of violation, charging it with failing to follow best management practices in controlling pollutants in storm water discharges from the construction sites. The notice also said the district had failed to develop a plan to reduce those pollutants.

On March 21, engineer Neill went out to inspect a second time. He found sediment running off railroad construction sites into the Loma Alta Creek near El Camino Real and Industry Street in Oceanside. That day it had rained 0.13 inches. On April 3, the board issued a second notice of violation.

The water quality board asked the transit district for two separate reports describing “corrections made at the project” to comply with its permit. The district filed those reports on April 6 and April 24, 2007, a self-inspection attesting that the violations had been corrected.

By August 31, Neill had completed a technical analysis of the Sprinter rail project. His report said the transit district had failed to conduct adequate inspections before and after the rainfalls that occurred around the time of his visits. The inspections were “critical to the foundation of an adequate program” to prevent future discharges.

He wrote that the district’s failures amounted to “a serious violation.” Having built a number of projects before, the report added, the transit district “should have the experience and expertise necessary” to comply with storm water requirements.

Neill also checked the district’s two April reports. He found them wanting.

The transit district, for example, said that temporary erosion control provided 100 percent coverage. Neill had found large areas, including steep slopes, with no controls.

The district reported that litter from work areas was collected and placed in watertight Dumpsters. Neill had found construction waste on open ground exposed to storm water runoff.

The transit district reported that storm drain inlets were properly protected. Not so, said Neill. Some drains had no protection at all.

“NCTD’s inspector either ignored items on the inspection checklist or was not properly trained…,” Neill’s report said.

Neill recommended that the transit district be fined the maximum amount — $10,000 for each violation for each day, a total of $160,000. A few weeks later, after waiving its right to a public hearing, the transit district paid the fine in full.

On October 5, Neill, accompanied by a second water quality board inspector, visited the rail project again, the first of six visits over two months to sites all along the line. They reported a host of new violations.

Heavy rains came in late November. The swollen Loma Alta Creek overflowed its banks, swamping businesses on Industry Drive. At Mission Linen Supply, office workers moved out of the flooded administrative building and into makeshift trailers raised more than two feet on rubber tires.

The transit district held a second party three days after Christmas, inviting VIPs to board two cars in Oceanside for a trip to Escondido. Less than an hour went by before the train whooshed through a banner arrayed across the tracks in downtown Escondido. The district said the line was set to carry paying customers — $2 one way and $4 for a pass to ride the entire day — on January 13.

The celebration was short-lived. On December 31, based on the inspections that had begun in October, the water quality board slapped the transit district with an order to clean up its mess. The order gave the district a month to show how it would stop the “existing and threatened pollution” from “unauthorized discharges” of sediment along the Sprinter right-of-way and from the project’s construction staging areas.

“I strongly urge a prompt and complete response…,” Michael P. McCann, assistant executive officer for the regional board, wrote Karen King, the transit district’s executive director. “Failure to meet these deadlines may subject you to further enforcement actions,” among them referral to the district attorney for criminal prosecution.

The board could also levy fines of $5000 per violation per day, McCann wrote, or seek an injunction against the district through the State Attorney General’s Office.

Around the same time, citing mounting frustration, Oceanside mayor Jim Wood resigned from the North County Transit District board. Fellow members of the nine-person board included city councilmen from the other cities along the line, San Marcos, Vista, and Escondido.

“I’ve had a lot of difficulties dealing with the North County Transit District,” the mayor explained in a phone interview. “I was really frustrated with them, frustrated to the point of yelling. Maybe in their rush to start up, they overlooked the issues.”

Mayor Wood and other Oceanside officials met with Industry Street business owners to discuss the flooding situation on Friday, January 4, amid forecasts of heavy weekend rains. The businesspeople blamed the flooding on the North County Transit District. They said that sediment deposited in the creek had cut the creek’s capacity about in half. Raising the rail bed to keep the creek from flooding the tracks had also caused heavy rains to pour onto their properties.

The City supplied the businesses with sandbags, but they were no match for that first major storm of the year. By Monday morning, water from the overflowing creek had risen more than two feet on some properties and deposited two and a half inches of mud and debris in parking lots.

Though Mission Linen Supply blockaded its office doors with 900 sandbags, the building flooded as much as 8 inches. Outside, the water rose in some places to 27 inches. It climbed over a 6-inch curb, painted yellow for caution, that separated an electrical transformer from a walkway. The transformer and several air compressors short-circuited. When the crew showed up for work at five on Monday morning, general manager Greg Rogers sent them home and shut down operations. “I’m not going to put my employees in harm’s way,” he said.

The mayor said he had never seen such flooding in that area; he said that the transit district kept denying it was “their issue and concern.”

A few hours later that Monday morning, the transit district started working on the track in Oceanside to prevent the creek from eroding the rail bed. By the following Saturday, the district had begun dredging the creek to increase its capacity. Some 1400 cubic yards of material were trucked off to the landfill. The work continued on January 13, scuttling the latest announced target for the Sprinter’s opening day.

District officials then set a new start date of January 27, though this time with a disclaimer. The Sprinter still needed to pass a safety inspection by the state Public Utilities Commission, which had a checklist of some 5000 items.

On January 25, that target date was moved up to March 9. Among the reasons: the doors of the train did not line up with the platform on the eastbound side at the Vista station. The platform was too far away from the track. To correct it would require removing, redesigning, and rebuilding the entire platform.

On January 26 and 27, it rained again, and the dredging seemed to have worked. This time, there was no appreciable flooding along Industry Street. District spokesman Tom Kelleher said the situation would improve even more when the City of Oceanside installed runoff basins to capture rainfall that might otherwise cause Loma Alta Creek again to overflow its banks. When that would be was unclear.

On January 31, the transit district responded to the violations found by water quality inspectors in October and November. In a report, the district said it had hired a consultant with experience in pollution remediation, the firm of Whitson Contracting and Management, to manage storm water compliance efforts.

Don Bullock, transit district manager of capital projects and construction, pledged that the district would install and maintain systems at Sprinter stations, staging areas, and storage yards “such that all discharges are minimized and/or contained.” Measures to control discharges would be in place at the “majority” of sites by March 1 and along the entire line by May 1.

Bullock also attested that the report and an abatement plan that went along with it, based on his “inquiry of the person or persons who manage the system or those persons directly responsible for gathering the information,” were “true, accurate, and complete.” He added, “I am aware that there are significant penalties for submitting false information, including the possibility of fine and imprisonment for knowing violation.”

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