Flushing Bay, one 11 waterways where the city’s plans for clean water need state approval. At issue is the science behind the state’s evaluation of those proposals. From the vantage point of a bike path or highway or pedestrian bridge, places like Flushing Bay, Westchester Creek or the Bronx River can look like water bodies everywhere, their cool blue-green surfaces rippled by wind and contoured by gentle currents. Whether those waters are “clean,” however, is a matter for science—and the subject of a complex legal dispute that hit federal court on Thursday. A coalition of environmental groups filed suit charging that the federal Environmental Protection Agency had failed to perform its duties under the Clean Water Act when it allowed New York State t use an outdated testing method to gauge whether New York City is doing enough to clean its waterways. “New York’s use of outdated standards will often indicate that water quality is suitable for contact recreation when in fact it is not,” the complaint filed in the Southern District by Riverkeeper, Natural Resources Defense Council and others, reads. “Thus, the standards will mislead the public and members of plaintiff organizations to believe that there is no significant risk of contracting waterborne diseases when in fact this risk is significant.” And that, the suit says, will put people “at increased risk of illness when they seek to use and enjoy” local waterways….