As the Panama Canal approached its fiftieth anniversary in the mid-1960s, U.S. officials concerned about the costs of modernization welcomed the technology of peaceful nuclear excavation to create a new waterway at sea level. Biologists seeking a share of the funds slated for radiological-safety studies called attention to another potential effect which they deemed of far greater ecological and evolutionary magnitude – marine species exchange, an obscure environmental issue that required the expertise of underresourced life scientists. An enterprising endeavor to support Smithsonian naturalists, especially marine biologists at the Smithsonian Tropical Research Institute in Panama, wound up sparking heated debates – between biologists and engineers about the oceans’ biological integrity and among scientists about whether the megaproject represented a research opportunity or environmental threat. A National Academy of Sciences panel chaired by Ernst Mayr failed to attract congressional funding for its 10-year baseline research program, but did create a stir in the scientific and mainstream press about the ecological threats that the sea-level canal might unleash upon the Atlantic and Pacific. This paper examines how the proposed megaproject sparked a scientific and political conversation about the risks of mixing the oceans at a time when many members of the scientific and engineering communities still viewed the seas as impervious to human-facilitated change.