Waters called Kaepernick "an American hero," and said it's the Kaepernicks of the world who will lead the U.S. in the future.
Maroon 5, Travis Scott and Big Boi are performing during the Super Bowl halftime show Sunday.
"I call on them to 'take a knee' onstage in full sight. I call upon them to do it in solidarity with Colin Kaepernick, to do it for every child shot to death on these mean streets, to do it for every bereaved mother and father and brother and sister," Waters said.
Kaepernick was the first pro athlete to take a knee during the national anthem at NFL games beginning in 2016 in protest over police brutality, and racial and social injustice.
Kaepernick, although a better quarterback than many of his peers, was not re-signed by San Francisco or any other team after the 2017 season. But after his protests, dozens of other athletes joined him in kneeling during the national anthem.