When President Obama took office in 2009, he put in place an executive order designed to prevent the abuses that took place during the Bush administration, which used waterboarding, extended sleep deprivation, standing in painful ”stress positions" on broken feet or legs, and the forced ”rectal feeding" of detainees carrying out hunger strikes over their conditions.
The executive order barred any ”officer, employee, or other agent" of the US government (whether military, CIA, FBI, or any other agency) from using any interrogation method that is not among those methods listed in US Army Field Manual, which contains detailed rules and guidelines for a wide range of procedures important to soldiers serving in the field. Since waterboarding and other ”enhanced interrogation techniques" favored by the Bush administration are not part of the Army Field Manual, they could no longer be used.
The problem is that those restrictions were part of an executive order, not an actual law passed by Congress, which means they could easily be overturned by the next president with an executive order of his own.
To prevent that from happening, the Obama administration worked with the Republican-controlled Congress in 2015 on legislation to make the rule about following the Army Field Manual part of actual US law. The legislation had strong bipartisan support, passing the Senate in an overwhelming vote of 91-3. It was meant to ensure that future presidents couldn't change the rules without going through Congress — but it contained a major loophole.
Robert Chesney, professor and associate dean at the University of Texas School of Law, explains on the Lawfare blog that there's nothing explicitly stopping the secretary of defense, who is appointed by the president, from changing what's in the Army Field Manual. Indeed, the law actually requires the Defense Department to "complete a thorough review" of the field manual every three years.
This means that the new secretary of defense could potentially push the Army to alter the Field Manual to include things like waterboarding in its list of approved interrogation techniques, thereby making all the safeguards President Obama put in place essentially meaningless.
Now, to be clear, this doesn't mean the US military or the CIA would actually be willing to use waterboarding, even if ordered to do so. Former top military brass and national security officials rejected Trump's comments during the campaign about potentially ordering the military to torture people and kill the families of suspected terrorists. (Trump later backed away from the latter idea, which would be a war crime.)
Current senior officers have been careful not to comment about Trump specifically to avoid wading into US domestic politics. But they've made clear that they're just as opposed to waterboarding or targeting the families of terrorists.
Chair of the Joint Chiefs of Staff Gen. Joseph Dunford, while explicitly refraining from discussing Trump directly, told the Senate Armed Services Committee in March that ”Those kinds of activities that you described are inconsistent with the values of our nation." Former CIA director Michael Hayden, who also led the National Security Agency from 1999 to 2005, told HBO's Bill Maher in February that if Trump were to order such actions once in office, ”the American armed forces would refuse to act."
Current CIA director John Brennan, speaking at an event at the Brookings Institution think tank back in April, stated, ”If a president were to order the agency to carry out waterboarding or something else, it'll be up to the director of CIA and others within CIA to decide whether or not that direction and order is something that they can carry out in good conscience," he said.
”As long as I'm director of CIA, irrespective of what the president says, I'm not going to be the director of CIA who gives that order. They'll have to find another director," he added.