MARBLEHEAD – A Marblehead boat company on Thursday admitted it dumped raw waste directly into North Shore waters in 2006, but still denies similar allegations dating back to 1990, including during Boston’s 2002 Fourth of July celebration.The Rockmore Company, Inc. pleaded guilty to two violations of the Rivers and Harbors Act and was criminally fined $225,000, according to the U.S. District Attorney’s office. The company also must pay $75,000 to the Massachusetts Environmental Trust as a “community service payment” to be used to fund water quality projects in the area, including Salem Harbor.”At the core, this is a public health issue, and from our perspective, the fines are about changing behavior and preventing pollution, which is always cheaper and efficient than any cleanup that can be engineered,” said Cindy Luppi, co-director of Clean Water Action New England in Boston.Attorney Peter Ball of Sally and Fitch LLP, who represents Rockmore, said the plea agreement is limited to a pair of incidents in 2006 and does not cover any earlier allegations. “The Rockmore Company has agreed to plead guilty to the two specific charges in the information, that is that on two dates in August 2006, the ‘Hannah Glover’ pumped sewage overboard into the navigable waters of the United States,” Ball said in a statement. “The Rockmore Company disputes many of other allegations in the information. As the matter pending in court, at this time we will reserve further comment.”According to court documents, Rockmore, which operates two vessels, one a restaurant boat docked in Salem Harbor and the other a dinner cruise ship and ferry boat, knowingly refused to pay for shore-side pump services when its sewage tank overflowed and instead discharged sewage along the shoreline. The sewage tanks on board were reportedly not large enough to hold the waste generated in the course of a trip and deck hands would pump the excess waste directly overboard. “Our society has goals of having fishable, swimmable public waters, because they are common resources and they are a big part of what makes Massachusetts what it is and gives our state its identity,” Luppi said. “We hope that the company and any others that might be engaged in similar behavior change going forward and it’ll be a better a day for the public that enjoy these waters.”Deck hands would pump the excess waste directly overboard, and in some cases, the waste from the “Rockmore,” the company’s boat restaurant docked in Salem Harbor, would be pumped onto the “Hannah Glover,” the company’s ferry and dinner cruise vessel, for later dumping. Additionally, from 2003 through 2005, the sewage tank on the “Rockmore” was allowed to overflow, causing seepage into the harbor as patrons continued to use the facilities.”The discharges took place at various locations along the Massachusetts coast, including in Salem Harbor and off beaches in Marblehead and Beverly, as well as in the Charles River near the Esplanade during the (Fourth of July) celebrations in 2002,” the federal lawsuit read.The company also must issue a full-page apology in three newspapers and is on probation for three years, during which it must adhere to strict sewage disposal guidelines.