The 49ers quarterback posted a photo to Instagram of cars caught in flood waters in Houston above the #7tormsComing hashtag that has become his trademark.
"I warned you the #7tormsComing !!! #Houston," the caption read.
After more than a foot of rain pounded the Houston area, several Twitter users commented the image was in poor taste before Kaepernick deleted it, although a tweet linking to it remained up.
The flooding has killed at least 14, with more declared missing.
Kaepernick apologized after the backlash and apologized on his Twitter account: "No disrespect intended! Prayers up!"
No disrespect intended! Prayers up!— Colin Kaepernick (@Kaepernick7) May 26, 2015
Another tweet followed that read, "Just livin! #WhoDoYouLove #IDontGetTired," and linked to a shirtless Instagram photo. It is not clear whether the tweet was related to the earlier one about flooding.
A few hours later, Kaepernick tweeted out another apology.