In a statement announcing the denial, the conservation department did not refer to the firestorm that had preceded its decision, aside from noting that it had received comments from more than 45,000 people about the project — 90 percent of whom opposed it. The department laid out its decision in technical terms, noting that construction would contaminate New York’s waters with mercury and copper.

“Construction of the NESE pipeline project is projected to result in water quality violations and fails to meet New York State’s rigorous water quality standards,” the department said, referring to what is formally called the Northeast Supply Enhancement pipeline.

While the pipeline had not attracted anywhere near the attention of the Keystone XL or Dakota Access pipelines that carry oil in the Great Plains region, within the insular world of New York politics it became a flash point in a larger debate about fighting climate change, spurring economic development and whether it was possible to marry the two.

Ahead of the decision, a chorus of Democratic elected officials denounced the pipeline, including the New York City comptroller, Scott M. Stringer, and Mayor Bill de Blasio. Hours before the decision was due on Wednesday, 11 United States representatives, including Jerrold Nadler, Alexandria Ocasio-Cortez and Hakeem Jeffries, wrote a letter to Mr. Cuomo in opposition.