The Sand Land mine near Southhampton, N.Y., resembles the cratered surface of the moon, a treeless, torn-up work site that underscores the demand for a vital, if often overlooked, natural resource.

Sand is crucial for building — it’s used to make concrete, asphalt and glass. And for over a century, sand from Long Island has helped build New York City’s skyline.

But under the mine, there is another precious commodity: an aquifer system that provides Long Island’s only source of drinking water. The nation is facing a groundwater crisis and Long Island, moreover, has a history of ignoring threats to its water until they become emergencies.

To avoid adding to that history, environmental activists and local government officials want Sand Land to close. The mining operation, they say, is cutting an open wound into the ground that could eventually taint the water underneath.

But sand mining has not damaged the region’s underground water supply, argue those in the business, while state regulators add that there is no reliable evidence of negative effects.

“There has never been an instance of a mine, whether it’s a hard rock mine in upstate New York or a sand and gravel mine on the island, seriously impacting the groundwater in any way,” said John Tintle, the owner of Sand Land.

Moreover, the sand mining industry employs some 175 workers — from laborers and machine operators to executives — who collect over $75 million in salaries on Long Island, said Marc Herbst, the executive director of the Long Island Contractors’ Association.

The tension in Southhampton, predated by more than a decade of legal fights, reflects the broader clash that has played globally between efforts to preserve natural resources and those promoting industry.

“This is one of the increasing number of instances where there are difficult trade-offs between legitimate environmental interests and important economic considerations,” said Michael Gerrard, a professor of environmental law at Columbia Law school.

Between 1865 and 1930, 100 million tons of sand arrived in Manhattan by barge from Long Island to build the Empire State Building, Rockefeller Center and other city landmarks. As Long Island sprouted towns and suburbs, however, the sand mining industry contracted and moved east. Today, there are 22 active sand mines on Long Island; down from over 70 during the industry’s heyday.

Sand mining is prohibited in Southampton, a municipality of about 70,000 residents in Suffolk County on Long Island. But Sand Land, which has been in operation since the 1960s, was grandfathered into the area’s zoning plans in the ’70s.

Around this time, dangerous toxins unrelated to sand mining were discovered in public wells on the island, prompting a slate of water-protection laws over the next 30 years. In 1991, one of these laws, unique to the region, ordered the New York State Department of Environmental Conservation to seek permission from municipalities before granting or amending sand mining permits.

Over the years, as Sand Land has attempted to make changes to its operations, this extra step has ignited some 20 years of litigation between Southampton, which has the backing of an influential environmental coalition that includes local lawmakers and nonprofits, and Mr. Tintle.

The latest major ruling was in February, when New York’s highest court annulled permits that included expansion requests that the Department of Environmental Conservation had issued to the mine without seeking the town’s approval. Sand Land was ordered to halt mining.

But since then, over 2,500 trucks, estimated to be carrying over 100 million pounds of sand, have left the mine, according to legal documents. Sand Land contends that it is removing stockpiled material, not excavating it.

The department, which is tasked with both supporting the mining industry and regulating it, has allowed the activity, deeming it legal over the objections of the town and the environmental coalition.

“D.E.C. is not choosing one side over the other as it pertains to groundwater versus mining,” said Sean Mahar, the department’s executive deputy commissioner.

And even as opponents of Sand Land insist that any operation at the mine violates court orders, the company has doubled down. In October, Sand Land requested permission to dig on an additional 11 to 12 of the property’s 50 acres.

“This is just the most recent example of Sand Land Corporation’s utter contempt for the environment and the rule of law,” said Brian J. Sexton, a lawyer representing the coalition.

The D.E.C. forwarded the mine’s request to the town. But regardless of what the town decides, the request appears destined to end up in court.

“That site still has a very long mining future ahead of it,” Mr. Tintle said.

Long Islanders live and work on top of their drinking water. So threats to it come in various forms, including septic waste (most homes in Suffolk County are not attached to a public sewer system) and toxic plumes, which are bodies of contaminated, underground water that can result from old military experiments, industrial spills and garbage landfills.

For much of the 20th century, businesses on Long Island “were careless and sloppy in how chemicals were handled and disposed of,” said Sarah Meyland, a groundwater expert who most recently headed the Center for Water Resources Management at the New York Institute of Technology.

Now, many Long Islanders are dealing with the results of those old industrial practices: dangerous man-made chemicals — not affiliated with sand mining — in their aquifers that are linked to a range of serious health risks, according to studies.

Sand Land sits over a special groundwater protection area, one of nine on Long Island. Water experts see these zones as the last line of defense for the island’s aquifers. Sand serves as an important filter, so excavating it removes a protective barrier.

Ron Paulsen, a hydrogeologist who used to run the groundwater investigative unit for the Suffolk County Department of Health Services, compared sand pits over aquifers to open wounds.

“Contaminants can get into your blood supply because there’s no skin there,” he said. “This is concerning because this was supposed to be a pristine water supply.”

In 2015, Mr. Paulsen, who is now a consultant, oversaw a groundwater test at Sand Land for Suffolk County. The concern at the time was the mine’s continued storage of vegetative waste like mulch and manure.

The study concluded that the handling of vegetative waste at Sand Land was a threat to the groundwater. Among other contaminants, it had elevated levels of nitrate, which comes from fertilizer and manure. Nitrate exposure in drinking water has been linked in some studies to an increased risk of infant death, and at high levels, to an elevated risk of cancer in adults.

Following the study’s publication, and several rounds in court, Sand Land was forced to stop storing vegetative waste. Mr. Tintle said the decision was voluntary.

Currently, the D.E.C. is conducting its own, three-year study on the effects of sand mining on groundwater in the area. But Ms. Meyland said it lacked rigor because, among other reasons, participation in the study is voluntary. Of the region’s 22 active mines, just four are taking part (Sand Land is not one of them).

In a statement, the D.E.C. called its study comprehensive.

The global demand for sand has reached about 50 billion metric tons per year, according to the United Nations, which has also predicted that water scarcity will be a major challenge in the 21st century. In parts of the world, the need for both resources is reaching crisis levels, the organization said.

This level of urgency could reach Long Island, which continues to face difficult compromises, several water experts said.

“It’s not that mining doesn’t have a place,” Mr. Paulsen said. “It’s where and how you do it.”