WASHINGTON — Two years ago, Gen. John F. Kelly, then head of the United States Southern Command, delivered a dire warning to Congress: The nation was not focusing on the security threat presented by the financial and operational relationship between terrorist networks and drug smuggling organizations.

“Terrorist organizations could seek to leverage those same smuggling routes to move operatives with intent to cause grave harm to our citizens or even bring weapons of mass destruction into the United States,” General Kelly said.

Now General Kelly, 66, is President-elect Donald J. Trump’s choice to lead the Department of Homeland Security, and his view of the threat to the southern border is likely to be the subject of questioning during his confirmation hearing on Tuesday.

The department, with a budget of more than $40 billion and more than 240,000 workers, is responsible for border security, immigration control, responding to natural disasters, cybersecurity and screening passengers at airports, among other duties.