The $3.8 billion Boston Harbor Project was substantially complete when the 9.5-mile outfall tunnel was commissioned in September of 2000. As components of the new Deer Island Wastewater Treatment Plant have come on-line, there have been corresponding improvements in the harbor’s water quality: advisories against swimming at most Boston Harbor beaches have declined, water clarity has improved markedly, contamination as monitored in the tissue of mussels from the harbor has been dropping for a decade, and marine species that inhabit the harbor have grown in numbers and diversity.