STOCKTON — A pair of giant water diversion tunnels proposed for the Sacramento-San Joaquin Delta could violate the federal Clean Water Act and increase harm to endangered fish species, according to the U.S. Environmental Protection Agency, which released its formal comment on the project Thursday. In a 43-page letter sent to the National Marine Fisheries Service, the EPA said its research found that by diverting freshwater from three new intakes proposed on the Sacramento River, the project is likely to increase concentrations of salinity, mercury, bromide, chloride, selenium and pesticides in the Delta. The estuary is habitat for species such as the endangered Delta smelt.