LYNN – Declaring it an “emergency,” Water and Sewer Commission executives are preparing to dispatch divers to patch holes in a section of a nearly three-mile-long outfall pipe running under Lynn Harbor.The cast-iron pipe carries fluid left over from the sewage treatment process in the Water and Sewer Commercial Street complex out to the ocean, where it is released in deep water. Fishing boat operators earlier this summer noticed bubbles on the ocean’s surface in an area roughly three-quarters of the distance along the pipe’s length.Commission Executive Director Daniel O’Neill said divers will descend into relatively shallow water between Lynn and Nahant to repair the holes. The holes are each roughly the size of a human hand.”It’s an emergency,” O’Neill said. “It will cost $25,000 to $30,000, (and) they will fix it in a week or so.”Constructed in 1925, the 14,000-foot pipe originally carried raw sewage out to the ocean.Environmental protection standards and improved sewage treatment technology means waste undergoes primary and secondary treatments in the Commercial Street facility before leftover liquid pours into the five-foot diameter pipe.”It’s essentially clean water, O’Neill said.Department of Environmental Protection spokesman Joseph Ferson acknowledged fluid running through the pipe is “fully treated effluent,” but he said the water must be discharged at the pipe’s ocean end so fluid can disperse in the widest-possible area and in deep water.”The concern is the system needs to operate properly,” Ferson said.