"Big water, ocean water", he said of Puerto Rico, for viewers not in the know.
But Carmen Yulin Cruz, the mayor of San Juan, heatedly denied that.
Presidential spokeswoman Sarah Huckabee Sanders said 10,000 government workers, including more than 7,000 soldiers, were helping Puerto Rico recover.
FEMA said this week that Puerto Rico has received 4.4 million meal kits, 6.5 million liters of water.
He screenshotted tweets in Spanish that were critical of the president, writing: 'San Juan, PR Mayor has been hating on @realDonaldTrump long before he was our President. This is the time to show our "true colors".
The mayor of Puerto Rico's capital city is accusing the Trump administration of inefficiency as the federal government continues to render aid to an island devastated by Hurricane Maria.
The U.S. Virgin Islands is exempt from the Jones Act. "We want them to be safe and sound and secure and we will be there every day until that happens".
Trump spokeswoman Sarah Huckabee Sanders said Mr Trump was responding to a request from Puerto Rico governor Ricardo Rossello, and that the waiver would go into effect immediately.
White House officials have rejected allegations the administration's Puerto Rico response hasn't measured up to that in Texas and Florida after earlier hurricanes Harvey and Irma.
Although Trump earlier this week cited Cruz in a tweet, thanking her for "your kind words" about the federal response, in fact Cruz has been critical nearly daily, saying officials are moving too slowly. Not fair to FR or effort!
Shaking her head, Cruz replied "well, maybe from where she's standing it's a good news story".
Acting Homeland Secretary Elaine Duke, center, is briefed on the Hurricane Maria response during a flight to Puerto Rico on Friday, Sept. 29, 2017.
"People can't fathom what it is to have children drinking from creeks, to have people in nursing homes without oxygen". When you don't have food for a baby, it's not a good news story.
Cruz then invited Duke to come witness the devastation of the towns and reconsider her statement.
"This is a "people are dying" story", she said in disbelief.
"This is a "people are dying" story, this is a life and death story, this is a truckload of stuff that can not be taken to people story", the mayor said on the verge of tears and sounding exhausted.