She then quickly backtracked and completed the jump which left her 50 metres behind the rest of the field.
Chepkoech, who finished fourth at the Rio Olympics, quickly made up the ground and put herself in the medal frame for the rest of the race.
Ironically she started to fade leading up to the water jump on the final lap.
Australia's Genevieve LaCaze wasn't surprised by the brain fade.
"It happens too often," she said. "It happens more and more in championship races because everyone's on edge.
"It barely ever happens in Diamond Leagues because you're just running for a time."
American Emma Coburn surged away over the final stages to take gold and end Kenya's recent dominance of the event.
Coburn went from third to first at the water jump to race away with the world title in a championships record of 9min04.03sec.
Her American teammate Courtney Frerichs took silver (9:03.77 sec) with Kenya's Hyvin Jepkemoi getting bronze (9:04.03 sec)
LaCaze got caught up in a fall early in the race where she had to hurdle another athlete which cost her badly and she faded to finish 12th in a season's best 9:26.25 sec.