WATERVILLE — Pan Am Railways will pay $152,000 in fines to settle allegations that it violated the federal Clean Water Act at its rail yards in Waterville and East Deerfield, Massachusetts.

The Billerica, Massachusetts-based company also will undertake an environmental culture assessment to reduce the environmental impact of rail operations at its five New England locations.

The settlement was announced Tuesday in a news release by the Environmental Protection Agency. The EPA filed an administrative complaint against Pan Am on Jan. 30. The original complaint asked for $375,000 in fines to resolve the violations.

The EPA alleged that the stormwater pollution prevention plan at Pan Am’s Waterville rail yard didn’t have the proper controls in place to minimize the effect of stormwater running off the site and into nearby waterways. Site visits revealed that the company also stored debris in piles on the site without proper controls in place, and oil staining was observed throughout the rail yard, according to the agency.

“Without adequate on-site controls, stormwater runoff can flow directly to the nearest waterway and cause water quality impairments such as siltation of rivers, beach closings, fishing restrictions, and habitat degradation,” the EPA said in its statement. “As stormwater flows over these sites, it can pick up pollutants, including sediment, biological and chemical oxygen demand and oil and grease.”

Pan Am also failed to implement a spill prevention, control and countermeasure plan fully at the site, a tool that is used to avoid oil spills.

“Every year, thousands of gallons of oil are spilled from oil storage facilities, polluting New England waters,” the statement continued. “Even the effects of smaller spills add up and damage aquatic life, as well as public and private property. Spill prevention plans are critical to prevent spills or, if they occur, adequately address them.”

The 100-acre rail yard along College Avenue is used to refuel and repair locomotives and store freight cars. It has a 110,000-gallon storage capacity for diesel fuel, lubricant, heating oil and waste oil. Almost half the capacity is in two 25,000-gallon tanks.

The EPA alleged similar violations at the company’s East Deerfield rail yard and that the company didn’t conduct stormwater inspections in 2011 and 2012 and failed to stabilize an area where there was significant erosion.

In addition to the financial penalties, Pan Am will undertake an environmental culture assessment and “develop and implement action plans to improve the environmental culture at five of its New England Facilities” in East Deerfield, Ayer and North Billerica, Massachusetts, and in Waterville and South Portland, according to the EPA.

“The goal of the ECA (environmental culture assessment) and action plans is to reduce the impact of rail operation on the environment,” the agency said in its statement.

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