Oscar Suarez and Magdalena Devil were both wearing life jackets when they went for a ride on a rented jet ski. They haven't been seen since.
A second meeting between Trump and Kim in Hanoi four months ago collapsed without any agreement.
Police said the gunman appears to have been either a disgruntled or former employee of the car dealership.
"Mackenzie, in the case you just want to be left alone, please let us know you are safe," police Assistant Chief Tim Doubt said.
The identities of those killed are being withheld until 24 hours after next of kin is notified, officials said.